chanana / coursenotes Goto Github PK

@morrowcj I started a new branch called A.
Your turn!

Tasks

1. Eliminate commas and quotes from second column of csv file:
   sed -E 's/"([0-9]+),([0-9]+),*([0-9]*)"/\1\2\3/' tableofSNPs.csv > out.csv

2. Check there are only three commas in each line:
   sed -E 's/[^,]//g' out.csv | sort | uniq
   The output should only contain one line consisting of 3 commas indicating a successful step 1.

Optional Tasks

3. Replace all A and T with T and A respectively:
   sed -E 'y/AT/TA/' tableofSNPs.csv > rev.csv

4. Check that the replacement was correct:
   sed -E s/'[^AT]'//g rev.csv | sort | uniq -c | tail -n 2 > countRev
sed -E s/'[^AT]'//g out.csv | sort | uniq -c | tail -n 2 > countOut
diff countRev countOut
   This is a three line solution. I don't know how to do a one-liner for this; please help.

Note: All commands were executed in macOS 10.14 (BSD)

@cecileane and @coraallencoleman

One really important thing I learned was how to undo changes in a repository. For example, if I have added something using git add <file>, then I can un-stage it using git reset HEAD <file>. I think this is a super useful feature to "undo" things.

@cecileane and @coraallencoleman

This script was written for python3 and tested on macOS 10.14

• The first line of the script is #! /usr/bin/env python3 which means it tries to use python3 by default. python3 no longer supports type long. This means that

$ ./binomial.py -n 150 -k 40
4408904561911885789946649584764715008

however, when it is run with python2 it will show

$ python ./binomial.py -n 150 -k 40
4.40890456191e+36

• The doctest module has problems with returning integers vs floating point values if run with python2

$ python ./binomial.py --test
testing the module...
**********************************************************************
File "./binomial.py", line 85, in __main__.choose
Failed example:
    choose(5, 3)
Expected:
    10
Got:
    10.0
**********************************************************************

Even though the code says

logChoose = logfactorial(n, k) - logfactorial(n - k)
    if log:
        return logChoose
    else:
        return round(math.exp(logChoose)) # returns whole number

@cecileane and @coraallencoleman