ERROR. vispr server *.vispr.yaml

[Patricia]

Hello,

I am following Wang et al 2019 workflow. I managed to run

snakemake --cores 8

successfully and it generates a *.vispr.yaml file that seems alright. However, when I try to run

vispr server results/*.vispr.yaml

to view the results the following error appears and I can’t move forward. Some help would be great. Thanks!

(mageck-vispr) BMO00501:results pcenteno$ vispr server *.vispr.yaml

/Applications/miniconda3/envs/mageck-vispr/lib/python3.6/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.

/Applications/miniconda3/envs/mageck-vispr/lib/python3.6/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)

Syntax error in config file rraPPC.vispr.yaml. Missing key "['neg|p-value', 'neg|fdr', 'neg|score'] not in index".

[masih]

Same problem here. @Patricia Did you find any solution?

[sama shamloo]

Hello,

I had the same error. I edited the files server.py and cli.py and then it worked.

go to this directory: /Applications/miniconda3/envs/mageck-vispr/lib/python3.6/site-packages/vispr/ and open the file server.py with a text editor (e.g. emacs) and go to line 23. change yaml.load(f) to yaml.safe_load(f)

Do the same for the file cli.py line 40.

This should solve the problems.

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