The Bash Shell

Exercise Answers

Files and Directories

Relative path resolution

Incorrect, since backup exists in the Users parent directory, where the preceding .. is referencing.
Incorrect, since .. is used before backup to reference the Users parent directory first, so ls will run on /Users/backup.
Incorrect as per 2, but also to have the directories have a following / we’d also need to use the -F flag.
Correct.

ls reading comprehension

This will attempt to list the contents of a file or directory called pwd which does not exist.
Partially correct, but 3 is also correct.
Partially correct, but 2 is also correct.
Correct.

Creating Things

Renaming files

Incorrect, since this would copy the mistakenly named file to another file with the desired name, but the original mistakenly named file will still exist.
Correct.
Incorrect, since this would not rename the file.
Incorrect, since mv is used to rename a file and cp is used to copy a file.

Moving and Copying

Incorrect, since proteins-saved.dat was created in the directory above, since .. was used before its filename when copying recombine/proteins.dat
Correct.
Incorrect, since proteins.dat was moved into the recombine directory.
Incorrect, since the recombine directory was created in this current directory.

Organizing Directories and Files

mv fructose.dat sucrose.dat analyzed will copy the files ending .dat into the analyzed directory.

Copy with Multiple Filenames

With several filenames and a directory, cp will copy the given files into the given directory.
When given three or more filenames, cp will return an error since with more than two arguments cp assumes the last argument is a directory.

Pipes and Filters

What does sort -n do?

sort -n will perform a sort interpreting numerical digits as proper numbers - a numerical sort. sort on its own will perform a sort assuming any numerical digits are just sequences of characters, e.g. 10 will come before 2 since 1 comes before 2.

What does >> mean?

> will redirect the output hello to the file testfile01.txt, replacing the contents of that file if it already exists.
<< will redirect the output hello to the file testfile01.txt, appending any existing content if that file already exists.

Piping commands together

Incorrect, since we cannot redirect to a command, we should use a | (pipe) instead.
Incorrect, since 1-3 when passed to head is interpreted as a file, not a range of line numbers.
Incorrect, since we need to sort the line counts before extracting the top three (otherwise we get them in whatever order wc gives them to head)
Correct.

Why does uniq only remove adjacent duplicates?

For efficiency. If it were to work across non-adjacent lines it would need to keep the whole file in memory in some way to know whether it had already encountered a line. This would need considerable memory with very large files, and searching for duplicate lines would take much longer to run.
You could use sort first in a pipe to sort the file contents to ensure duplicate lines are adjacent, e.g. sort salmon.txt | uniq

Pipe reading comprehension

cat animals.txt will output the contents of animals.txt.
head -5 accepts the output from cat and output the first 5 lines of that.
tail -3 accepts the 5 lines from head and output the last 3 lines of that.
sort -r accepts the 3 lines from tail and output those lines in reverse sort order.
> final.txt will take the output from sort and redirect it into a file called final.txt.

Shell Scripts

Variables in shell scripts

Incorrect, since -1 is passed to head in the script it will output the first line of each .pdb file, whilst the -1 passed to tail will output the last line of each .pdb file.
Correct.
Incorrect, since *.pdb is passed into the script and used by head and tail, so only .pdb files will be used.
Incorrect, since the quotes only mean that *.pdb will be passed into the script without expansion.

Script reading comprehension

Script 1 will output a list of files that match the *.* pattern, i.e. fructose.dat, glucose.dat, and sucrose.dat.
Script 2 will take in three arguments on the command line, and for each of them, print out their contents.
Script 3 will print out all arguments as passed to the script on a single line and append .dat to that output.

Loops

Variables in Loops

The first loop will present “fructose.dat glucose.dat sucrose.dat” three times, since we are running ls *.dat three separate times - we’re not making use of the loop variable $datafile. The second loop will produce “fructose.dat”, “glucose.dat”, and “sucrose.dat” (each on a separate line) since we’re passing $datafile to ls.

Saving to a File in a Loop - Part One

Correct.
Incorrect, since we’re using the > redirect operator, which will overwrite any previous contents of xylose.dat.
Incorrect, since the file xylose.dat would not have existed when *.dat would have been expanded.
Incorrect.

Saving to a File in a Loop - Part Two

Correct.
Incorrect, since we’re looping through each of the other .dat files (fructose.dat and glucose.dat) whose contents would also be included.
Incorrect, since maltose.txt has a .txt extension and not a .dat extension, so won’t match on *.dat and won’t be included in the loop.
Incorrect, since the >> operator redirects all output to the sugar.dat file, so we won’t see any screen output.

Doing a dry run

Version 2 is the one that successfully acts as a dry run. In version 1, since the > file redirect is not within quotes, the script will create three files analyzed-basilisk.dat, analyzed-minotaur.dat, and analyzed-unicorn.dat which is not what we want.

Finding Things

Using grep

Incorrect, since it will find lines that contain of including those that are not a complete word, including “Software is like that.”
Incorrect, -E (which enables extended regular expressions in grep), won’t change the behaviour since the given pattern is not a regular expression. So the results will be the same as 1.
Correct, since we have supplied -w to indicate that we are looking for a complete word, hence only “and the presence of absence:” is found.
Incorrect. -i indicates we wish to do a case insensitive search which isn’t required. The results are the same as 1.

find pipeline reading comprehension

Find all files (in this directory and all subdirectories) that have a filename that ends in .dat, count the number of files found, and sort the result. Note that the sort here is unnecessary, since it is only sorting one number.

Matching ose.dat but not temp {}:

Incorrect, since the first grep will find all filenames that contain ose wherever it may occur, and also because the use of grep as a following pipe command will only match on filenames output from find and not their contents.
Incorrect, since it will only find those files than match ose.dat exactly, and also because the use of grep as a following pipe command will only match on filenames output from find and not their contents.
Correct answer. It first executes the find command to find those files matching the ’*ose.dat’ pattern, which will match on exactly those that end in ose.dat, and then grep will search those files for “temp” and only report those that don’t contain it, since it’s using the -v flag to invert the results.
Incorrect.

Additional Exercises

Copying files with new filenames

Assuming the output directory is named copied:

today_date=$(date +"%d-%m-%y")

for file in data/*.csv
do
    base_file=$(basename $file)
    cp $file copied/$today_date-$base_file
done

Filtering our output

The Max_temp_jul_F column is the fourth column in each data file
Assuming the input directory is named copied and the output directory is named filtered:

for file in copied/*.csv
do
    base_file=$(basename $file)
    cat $file | cut -d"," -f 4 > filtered/$base_file
done