Marra2014_pseudo.md

Hints and pseudo code for Exercise 1.10.1 (data from Marra and DeWoody, 2014)

1. To change the directory, you can use the commands explained at page 20.
2. To find the size of a file you can use a modifier of the command ls.
3. To copy a file, see page 22.
4. Is there a grep option that counts the number of occurrences?
5. To replace single characters, you can use the command tr with its options and modifiers.
6. You can use grep to match any line containing the word isogroup; then use cut to isolate the part detailing the isogroup; finally, you want to remove the duplicates (e.g., page 32) and count.
7. Again, you can use a combination of grep and cut to extract the contig names and read counts; the command sort allows you to choose the delimiter as well as ordering numeric values.