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yoavram / curveball

Predicting microbial growth in a mixed culture from growth curve data
http://curveball.yoavram.com
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error with strain and cycle number #153

Closed pavlo888 closed 4 years ago

pavlo888 commented 4 years ago

Hi,

I am very interested in using this tool for analysis but I am getting an error when trying to run the test data from the tutorial.

I have installed the package in a Conda environment using python3. When I run the following command:

curveball analyse Tecan_280715.xlsx --plate_file=G-RG-R.csv --ref_strain=G

I get the following error:

/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/seaborn/axisgrid.py:243: UserWarning: Thesizeparameter has been renamed toheight`; please update your code. warnings.warn(msg, UserWarning)

Traceback (most recent call last): File "/Users/pablo/opt/anaconda2/envs/curveball/bin/curveball", line 8, in sys.exit(cli()) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/click/core.py", line 829, in call return self.main(args, kwargs) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/click/core.py", line 782, in main rv = self.invoke(ctx) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/click/core.py", line 1259, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/click/core.py", line 1066, in invoke return ctx.invoke(self.callback, ctx.params) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/click/core.py", line 610, in invoke return callback(args, **kwargs) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/curveball/scripts/cli.py", line 254, in analyse file_results = _process_file(filepath, plate, blank_strain, ref_strain, max_time, guess, param_min, param_max, param_fix, weights, ci, nsamples) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/curveball/scripts/cli.py", line 304, in _process_file g = curveball.plots.plot_strains(df, output_filename=strains_plot_fn) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/curveball/plots.py", line 131, in plot_strains grp = data.groupby(by=by) File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/pandas/core/frame.py", line 5801, in groupby return groupby_generic.DataFrameGroupBy( File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/pandas/core/groupby/groupby.py", line 402, in init grouper, exclusions, obj = get_grouper( File "/Users/pablo/opt/anaconda2/envs/curveball/lib/python3.8/site-packages/pandas/core/groupby/grouper.py", line 598, in get_grouper raise KeyError(gpr) KeyError: ('Strain', 'Cycle Nr.')`

Could you please help me solve this issue?

Thanks.

Pablo

yoavram commented 4 years ago

Someone else just notified me about this via email. I’ll try to figure it out soon after the holiday.