Getting Around

Challenges

Please refer to the following figure when answering the challenges below.

Figure 1

If pwd displays /users/thing, what will ls ../backup display?

1. ../backup: No such file or directory
2. 2012-12-01 2013-01-08 2013-01-27
3. 2012-12-01/ 2013-01-08/ 2013-01-27/
4. original pnas_final pnas_sub

If pwd displays /users/fly, what command will display

1. thesis/ papers/ articles/
2. ls pwd
3. ls -r -F
4. ls -r -F /users/fly
5. Either #2 or #3 above, but not #1.

What does the command cd without a directory name do?

1. It has no effect.
2. It changes the working directory to /.
3. It changes the working directory to the user's home directory.
4. It is an error.

We said earlier that spaces in path names have to be marked with a leading backslash in order for the shell to interpret them properly. Why? What happens if we run a command like:

$ ls my\ thesis\ files

without the backslashes?

Creating Things

Challenges

  1. What is the output of the closing ls command in the sequence shown below?
$ pwd
/home/thing/data
$ ls
proteins.dat
$ mkdir recombine
$ mv proteins.dat recombine
$ cp recombine/proteins.dat ../proteins-saved.dat
$ ls

  1. Suppose that:

    $ ls -F
analyzed/  fructose.dat    raw/   sucrose.dat

What command(s) could you run so that the commands below will produce the output shown?

$ ls
analyzed   raw
$ ls analyzed
fructose.dat    sucrose.dat

  1. What does cp do when given several filenames and a directory name, as in:

    $ mkdir backup
$ cp thesis/citations.txt thesis/quotations.txt backup

  2. Why do you think cp’s behavior is different from mv’s?

  3. The command ls -R lists the contents of directories recursively, i.e., lists their sub-directories, sub-sub-directories, and so on in alphabetical order at each level. The command ls -t lists things by time of last change, with most recently changed files or directories first. In what order does ls -R -t display things?

Pipes and Filters

Challenges

  1. What is the difference between:

    wc -l < *.dat

    and:

    wc -l *.dat

The command uniq removes adjacent duplicated lines from its input. For example, if a file salmon.txt contains:

coho
coho
steelhead
coho
steelhead
steelhead

then uniq salmon.txt produces:

coho
steelhead
coho
steelhead

Why do you think uniq only removes adjacent duplicated lines? (Hint: think about very large data sets.) What other command could you combine with it in a pipe to remove all duplicated lines?

  1. A file called animals.txt contains the following data:

    2012-11-05,deer
2012-11-05,rabbit
2012-11-05,raccoon
2012-11-06,rabbit
2012-11-06,deer
2012-11-06,fox
2012-11-07,rabbit
2012-11-07,bear

Fill in the table showing what lines of text pass through each pipe in the pipeline below.

cat animals.txt        |    head -5 |   tail -3 |   sort -r >   final.txt

  1. The command:

    $ cut -d , -f 2 animals.txt

    produces the following output:

    deer
rabbit
raccoon
rabbit
deer
fox
rabbit
bear

    What other command(s) could be added to this in a pipeline to find out what animals have been seen (without any duplicates in the animals’ names)?

Loops

Challenges

  1. Suppose that ls initially displays:

    fructose.dat    glucose.dat   sucrose.dat

    What is the output of:

for datafile in *.dat
do
    ls *.dat
done

In the same directory, what is the effect of this loop?

for sugar in *.dat
do
    echo $sugar
    cat $sugar > xylose.dat
done
  1. Prints fructose.dat, glucose.dat, and sucrose.dat, and copies sucrose.dat to create xylose.dat.
  2. Prints fructose.dat, glucose.dat, and sucrose.dat, and concatenates all three files to create xylose.dat.
  3. Prints fructose.dat, glucose.dat, sucrose.dat, and xylose.dat, and copies sucrose.dat to create xylose.dat.

  4. None of the above.

  5. The expr does simple arithmetic using command-line parameters:

    $ expr 3 + 5
8
$ expr 30 / 5 - 2
4

Given this, what is the output of:

for left in 2 3
do
    for right in $left
    do
        expr $left + $right
    done
done

  1. Describe in words what the following loop does.

    for how in frog11 prcb redig
do
$how -limit 0.01 NENE01729B.txt
done

Shell Scripts

Challenges

  1. Leah has several hundred data files, each of which is formatted like this:

    2013-11-05,deer,5
2013-11-05,rabbit,22
2013-11-05,raccoon,7
2013-11-06,rabbit,19
2013-11-06,deer,2
2013-11-06,fox,1
2013-11-07,rabbit,18
2013-11-07,bear,1

  2. Write a shell script called species.sh that takes any number of filenames as command-line parameters, and uses cut, sort, and uniq to print a list of the unique species appearing in each of those files separately.

  3. Write a shell script called longest.sh that takes the name of a directory and a filename extension as its parameters, and prints out the name of the most recently modified file in that directory with that extension. For example:

    $ bash largest.sh /tmp/data pdb

    would print the name of the PDB file in /tmp/data that has been changed most recently.

  4. If you run the command:

    history | tail -5 > recent.sh

    the last command in the file is the history command itself, i.e., the shell has added history to the command log before actually running it. In fact, the shell always adds commands to the log before running them. Why do you think it does this?

  5. Joel’s data directory contains three files: fructose.dat, glucose.dat, and sucrose.dat. Explain what each of the following shell scripts does when run as bash scriptname *.dat.

1.        echo *.*
2.  
for filename in $1 $2 $3
do
    cat $filename
done
3.  
echo $*.dat

Finding Things

Challenges

  1. The middle.sh script’s numerical parameters are the number of lines to take from the head of the file, and the number of lines to take from the tail of that range. It would be more intuitive if the parameters were the index of the first line to keep and the number of lines, e.g., if:

    $ bash middle.sh somefile 50 5

    selected lines 50-54 instead of lines 46-50. Use $() and the expr command to do this.

  2. Write a short explanatory comment for the following shell script:

    find . -name '*.dat' -print | wc -l | sort -n