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Create a standalone Python program¶
The instructions for this exercise are in this Jupyter notebook, but to successfully complete the exercise, you need to write a plain Python .py file called plot_pcr_data.py that runs from the command line. Write your program so that when you run it like this:
python plot_pcr_data.py pcr_sample_1.csv
It will read load the CSV file named pcr_sample_1.csv and save a plot called pcr_sample_1.csv.png. This data file is the result of a real-time PCR experiment in a 6 well plate. The plot should plot number of cycles on the X axis and fluorescence intensity on the Y axis. There should be a line for the data from each well in the experiment.
Hints:
- Remember that you can get the command-line arguments to a python program by importing the
sysmodule and accessing thesys.argvvariable, which is a list of strings. So the filename with the data is provided as a command-line argument to your python program. - Read the CSV data from the provided filename using Pandas
read_csv()function. - Plot the results with seaborn's
lineplot()function. - Save this figure (with matplotlib.pylot's
savefig()) to a file with the name equal to the original file name with.pngappended to it (e.g. for the above example withpcr_sample_1.csvas input, save the figure topcr_sample_1.csv.png).
When you are done with your program plot_pcr_data.py, upload it to the directory for this exercise. I will run it with a new CSV data file from a different PCR experiments to check that it works.
With pcr_sample_1.csv, your plot should look like this:
