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Tool for estimating growth rates from microbial growth curves

License: Other

Python 100.00%
bioinformatics biology growth-curves curve-fitting

croissance's People

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green2013tea meono klbio ds-heejae yangluom atha-tsagkadouras laeblab piyushnanda-sysbio ettm-software persat-lab tazomatalax

croissance's Issues

duplicate rows in results and missing start/end

using command line interface seems to result in duplicate row as below:

name	phase	slope	intercept	N0	SNR	rank
A1	0	0.34830052058623445	-2.0915407235239205	26.691788231631115	308.5905617858235	100.0
A1	1	0.34830052058623445	-2.0915407235239205	26.691788231631115	308.5905617858235	100.0

also start and end for phases are missing.

handling minutes as time unit

When using process_curve on notebooks with time given in minutes (all int, if i remember right), I noticed no growth curve/phase can be found. Just converting minutes to hour resolves the issue.

Unable to generate figure

I am facing the following error. Need your guidance

sajjad@sajjad-ThinkStation-P910:~/Downloads$ croissance --figures hhh.tsv
2022-11-28 09:39:48 croissance INFO Reading curves from 'hhh.tsv
2022-11-28 09:39:48 croissance INFO Collected a total of 8 growth curves
2022-11-28 09:39:48 croissance INFO Annotating growth curves using 1 threads
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '0':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '600':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '1200':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '1800':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '2400':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '3000':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '3600':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance ERROR Unhandled exception while annotating '4200':
2022-11-28 09:39:48 croissance ERROR Traceback (most recent call last):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/main.py", line 44, in call
2022-11-28 09:39:48 croissance ERROR name=name,
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 125, in estimate_growth
2022-11-28 09:39:48 croissance ERROR for phase in _find_growth_phases(smooth_series, window=n_hours):
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/init.py", line 186, in _find_growth_phases
2022-11-28 09:39:48 croissance ERROR first_derivative = savitzky_golay(curve, window, 3, deriv=1)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/anaconda3/lib/python3.7/site-packages/croissance/estimation/util.py", line 15, in savitzky_golay
2022-11-28 09:39:48 croissance ERROR index=series.index, data=savgol_filter(series.values, *args, **kwargs)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 335, in savgol_filter
2022-11-28 09:39:48 croissance ERROR coeffs = savgol_coeffs(window_length, polyorder, deriv=deriv, delta=delta)
2022-11-28 09:39:48 croissance ERROR File "/home/sajjad/.local/lib/python3.7/site-packages/scipy/signal/_savitzky_golay.py", line 97, in savgol_coeffs
2022-11-28 09:39:48 croissance ERROR raise ValueError("polyorder must be less than window_length.")
2022-11-28 09:39:48 croissance ERROR ValueError: polyorder must be less than window_length.
2022-11-28 09:39:48 croissance INFO Writing annotated curves to 'hhh.output.tsv'
2022-11-28 09:39:48 croissance INFO Writing PDFs to 'hhh.output.pdf'
2022-11-28 09:39:48 croissance INFO Done ..

input1.txt

Identified exponential phases seem to cover lag phase

I applied croissance to analyze growth curves of Pseudomonas aeruginosa grown on glycerol and the exponential phases identified by Croissance seem to include lag phases (and gives 0 lag time). I have attached a figure where the identified exponential phases are shown in shaded blue (rank 1st) and shaded green (rank 2nd). You might see that in most cases, the identified exponential phase is extended to the origin of time and thus includes lag phase. Technically, I constrained n0 to be zero and the y axis was plotted on the log scale. Do you think this is an issue and, if it is, what causes it?

growth_curve_PA

missing example.tsv file?

I cannot find a file named example.tsv in the repository, but one is mentioned in the README.rst file. Should the repository contain this example file?

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