Error while running vispr server results/*.vispr.yaml

[simarjot singh]

I am getting a this error despite reverting to panda 0.19.2:

Loading data. /home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/target.py:32: RuntimeWarning: divide by zero encountered in log10 self.df["log10-p-value"] = -np.log10(self.df["p-value"]) Traceback (most recent call last): File "/home/simarjot/miniconda3/bin/vispr", line 6, in <module> sys.exit(vispr.cli.main()) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 207, in main init_server(*args.config, host=args.host, port=args.port) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/cli.py", line 42, in init_server app.screens.add(config, parentdir=os.path.dirname(path)) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 29, in add self.screens[screen] = Screen(config, parentdir=parentdir) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 76, in init get_path(config["targets"]["results"])) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in parse_target_results for condition in conditions File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 147, in <dictcomp> for condition in conditions File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 145, in <dictcomp> for selection in selections File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/init.py", line 139, in get_results return target.Results(res.copy(), table_filter=table_filter) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/vispr/results/target.py", line 45, in init pval_cdf = pval_cdf.value_counts(normalize=True, sort=False, bins=1000).cumsum() File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/core/base.py", line 951, in value_counts normalize=normalize, bins=bins, dropna=dropna) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/core/algorithms.py", line 365, in value_counts cat, bins = cut(values, bins, retbins=True) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/tools/tile.py", line 119, in cut include_lowest=include_lowest) File "/home/simarjot/miniconda3/lib/python3.6/site-packages/pandas/tools/tile.py", line 194, in _bins_to_cuts raise ValueError('Bin edges must be unique: %s' % repr(bins)) ValueError: Bin edges must be unique: array([0., 0., 0., ..., 0., 0., 0.])

[JD56]

Hi, I was able to get pass the error simply by modifying the config.yaml file, surrounding the trim-5 number with double quotes (instead of 25 in the test config file, it is now "25") and doing the same with the sgRNA length (len) number. Doing so is indicated in the config file from test data starting from step 2 but not in the one starting from step 4, might be a good idea to add it there just in case Hope this helps