AMiGA : Get Time at Threshold

In your analysis, you may be interested in detecting the time at which growth curves reach a certain OD threshold. The get_time functions can detect these time intervals from the predicted growth curves. Let’s say that you fit a Biolog PM plate with AMiGA.

python amiga.py fit -i /home/outbreaks/erandomii/ER1_PM2-1.txt --save-gp-data

Here, the --save-gp-data will save a file that includes the growth curves and various variations of it. See Command-line interface for more details. It will include for example a column titled OD_Growth_Fit which is the predicted log growth converted back real OD but still baseline-corrected (i.e. first measurement is approximately zero).

Let’s say that you are interested in find out when does the growth curve in each well reach an OD of 0.5. The get_time can do this with the following.

python amiga.py get_time --gp-data /home/outbreaks/erandomii/gp_Data/ER1_PM2-1_gp_data.txt --summary /home/outbreaks/erandomii/summary/ER1_PM2-1_summary.txt --threshold 0.5 --curve-format OD_Growth_Fit 

Here, we asked AMiGA to find out when does the OD_Growth_Fit for each curve reaches an OD of 0.5. To do this, we needed to point AMiGA to both the file that contains OD_Growth_Fit and the summary file which contains meta-data. AMiGA will then update the summary file to include a new column t_od(0.5) which indicate the time needed to reach OD of 0.5. If the growth curves started at OD higher than 0.5, then the value will be zero. If the growth curve never reaches an OD of 0.5, the the value will be inf or infinity.

Command-line arguments

To see the full list of arguments that amiga compare will accept, run

python amiga.py get-time --help

which will return the following message

usage: amiga.py [-h] --gp-data GP_DATA --summary SUMMARY --threshold THRESHOLD
                [--curve-format {OD_Data,OD_Fit,GP_Input,GP_Output,OD_Growth_Fit,OD_Growth_Data,GP_Derivative}]

Get time at which OD reaches a certain value

optional arguments:
  -h, --help            show this help message and exit
  --gp-data GP_DATA
  --summary SUMMARY
  --threshold THRESHOLD
  --curve-format {OD_Data,OD_Fit,GP_Input,GP_Output,OD_Growth_Fit,OD_Growth_Data,GP_Derivative}

See more details for these arguments in Command Line Interface

AMiGA Anaylsis of Microbial Growth Assays

Get Time at Threshold

Command-line arguments