hypatiayu/caltech-bootcamp-projects-

Projects for Caltech Introduction to Programming for the Biological Science Bootcamp (June 2019)

caltech-bootcamp-projects-'s Issues

General notes on style

The first thing that jumped out to me when I looked at your code was your style. It's not bad, but it can be better with a few easy changes in habit.

I recommend skimming the Google Python Style Guide, and learning how to use a python linter, which will automatically flag style issues (and other things).

Honestly, I can't remember if I've ever used Pylint, but I suspect it is probably good enough for your purpose.

So, I recommend you install and run pylint, and then make the suggested changes to your code.

Get involved in the coding community!

Learning programming is easiest when you have people to lean on, so I would recommend involving yourself in the coding community for the best long-term education.

• Hacker News, Silicon Valley's newspaper
• Stack Overflow, where most of your questions are answered
• Consider joining your local chapter of Women Who Code
• Check Meetup for their various monthly and bi-weekly coding groups
• Use LeetCode to practice coding problems, and KhanAcademy for general computer science principles and programming courses
• Check out /r/cscareerquestions
• Try to make your own website with GitHub Page's free website hosting and the Khan Academy website tutorial! (This is how I first learned HTML/JS/CSS.) You can check out my website repo as an unnecessarily-complicated example.
• Revamp your Python experience with Sublime Text 3 (instead of using Anaconda / Jupyter, which tends to be a bit 'heavier'.) I use Sublime in my day-to-day workflow

Create a README.md

I would like to see a README.md, which is a Markdown file that goes in project file to explain what the project is, and how to use it.

• Make A README
• Markdown Cheatsheet
• Example README from my forked version of Justin's bootcamp repo.

BTW, Github does a pretty smart thing by automatically displaying READMEs on the home page of repositories. If you go to the home page of my forked bootcamp repository and scroll down, you can see the README without clicking on it.

Very large cell

In Mining_Salmonella_Genome.ipynb, cell Out[15] is too large. Can you reduce the amount of output?

All-caps in variables / file names

This will probably be covered by the style guide + linter, but I just want to make special mention that I would personally avoid using many ALL_CAPS for file names and variable names (unless it's a static variable). There's some pretty hot discussion about what the best naming style is, but I personally find the frequent use of all-caps harder to read.

Using simple for loops

In LONGEST_ORF_FINDER.ipynb, we have:

def ORF_LIST(LIST):
    
    """Make a list of all of the open reading frames"""
    
    #Make a list of the locations of all the ATG start sites
    ATG_INDEX_LIST = ATG_INDEX(LIST)
    
    #List to store each of the Open reading frames
    ORFS = []

    #Iterate through the list of ATG start sites, to add it to the ORF_LIST one by one
    for i in range(0, len(ATG_INDEX_LIST)):
        START_INDEX = ATG_INDEX_LIST[i]
        ORF = OPEN_READING_FRAME(START_INDEX, LIST)
        ORFS.append(ORF)
    
    #Return the list of open reading frames 
    return(ORFS)

I think you can simplify the iteration using this format:

for start_index in atg_index_list:
        ORF = OPEN_READING_FRAME(START_INDEX, LIST)
        ORFS.append(ORF)