Assignment 2. Summary. Some Important bash Instructions. CSci132 Practical UNIX and Programming Assignment 2, Fall Prof.

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1 Assignment 2 Summary The purpose of this assignment is to give you some practice in bash scripting. When you write a bash script, you are really writing a program in the bash programming language. In class I explained that bash is not just a shell, but a programming language as well, and a bash script can just as well be called a bash program. I mention this now because very soon you will begin writing programs in another programming language, Perl, and this is the rst in a sequence of small steps in mastering Perl. We have been calling your programs shell scripts. A script is a program, make no bones about it. Scripts are programs written in a scripting language, which is a special kind of programming language. All scripting languages are programming languages, but not vice versa. The distinction will be explained in a later lecture. I will call bash both a programming language and a scripting language. This assignment will begin with a review of some of the things that have been covered in class, and then introduce a few things that were not covered in class. Some Important bash Instructions A bash instruction is also called a statement. For example, the if-instruction if test $# -ne 2 then echo usage: $0 arg1 arg2 exit fi is usually referred to as the if-statement. From this point forward, I will call instructions statements. The bash programming language has several statements that are known as looping statements. A looping statement is one that makes it possible to repeat a sequence of statements one or more times. In class we covered the while-statement too: the while-statement is a looping statement whose form (syntax ) is while <expression> <list-of-statements> ne in which <expression> is a statement such as the test command, or any other statement that can be evaluated as being true or false, and <list-of-statements> is any sequence of statements (including looping statements.) The following snippet (little piece) of a script shows one example of a while-statement: This is licensed under the Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. To view a copy of this license, visit 1

2 echo -n "Try to guess my favorite color:" read guess rest_of_line mycolor=`cat secretfile` # read about backquoted commands like `cat file` while [ $guess!= $mycolor ] echo -n "Sorry, that is not my favorite color. Try again: " read guess rest_of_line ne In the above script, the <expression> part of the while-statement is [ $guess!= $mycolor ] and the <list-of-statements> is the list of two lines echo -n "Sorry, that is not my favorite color. Try again: " read guess rest_of_line The above script will test whether guess is the same string as mycolor, and if it is not, it will execute the echo and read statements and then re-evaluate the test command that compares guess and mycolor. It will keep ing this until the user enters a string that is identical to the string stored in mycolor. When she es, the expression becomes false and the while loop is exited. A while-statement is usually called a while loop because if we visualize the sequence of executed statements as being connected by an imaginary thread, then this thread loops around and around the lines of the script. Bash also has a for-loop. (It has other loops too that I will not discuss here.) The for-loop is very dierent from the while-loop. It has two forms. One form (again the proper term is syntax ) is for <variable> in <argument-list> <list-of-statements> ne and the other is for <variable> <list-of-statements> ne The <variable> can be any valid variable name (words starting with letters and containing letters, digits, and the underscore character.) The <argument-list> can be any sequence of words, including words that look like numbers. Examples of this are for number in for name in John Jacob Judy Jocelyn for word in $* As you can see, this can be very powerful. As with the while-loop, the list of statements is any list of statements, but the intention is that the variable plays a role in this list. For example, the script let sum=0 for number in let square=$number*$number let sum=$sum+$number echo The square of $number is $square ne echo The sum of the numbers is $sum. 2

3 displays ten lines showing the squares of the rst ten positive integers and then displays their sum. Notice how the sum is calculated. The second form of the for-loop es not need an argument list. It automatically assigns to the variable the successive words from the command line arguments of the script when it is run: for word echo $word. ne It is the same as for name in $* echo $word. ne It just prints the words found on the command line one after the other on separate lines. Tasks This assignment consists of two exercises in writing relatively simple shell scripts. writing any script are The objectives when clarity eciency simplicity the script should be easy to understand by someone with a basic knowledge of UNIX; the script should use the least resources possible; and the script should be as simple as possible. An example will demonstrate. Suppose we needed a script that would count the number of lines in a le named molecule containing the word 'ATOM' anywhere on the line. The following script would achieve this: #!/bin/bash grep ' ATOM ' molecule > atomcount wc -l atomcount > answer rm atomcount cat answer rm answer but it is very inecient (because it needlessly creates les and then removes them), it is hard to understand because the reader spends more time reading it and may not be familiar with certain operators such as >, and it is not as simple as it could be. A simple, well-cumented, and ecient solution is #!/bin/bash # Displays how many lines in file molecule contain ATOM as a complete word # Written by Stewart Weiss grep -c ' ATOM ' molecule # The -c option to grep counts matching lines It has comments to explain what it es and it achieves it with a single command that can be looked up easily. Your job is to apply these ideas as you create solutions to the following exercises. 3

4 1. The last command lists information about who has logged into the computer on which it is run. In particular, it has a column with the username, the terminal on which the user was connected, the internet address (the IP address) from which they connected to the computer, and the date and time that they logged in and then logged out if they did. If they logged out it also displays the total time they were logged in. For example, this is an entry for me on cslab12: sweiss pts/ Thu Sep 14 13:05-14:27 (01:22) If the username is too long it is truncated, but there are options to display the full username. For this exercise you are to write a bash script named logincount that takes a list of usernames as its command line arguments and displays on the screen, for each user name, a message of the form Number of times that <username> logged into this machine is <N > where <N> is to be replaced by the number of records that the last command output that match <username> exactly. For example, if I enter the command logincount sweiss it should output something like Number of times that sweiss logged into this machine is 7 If a name given as an argument is not a username, nothing is printed for that name. On the other hand, if no names are given, it is an error and the command should display the error message, Usage: logincount <list of usernames>. 2. A DNA string is a sequence of the letters a, c, g, and t in any order. For example, aacgtttgtaaccag is a DNA string of length 15. Each sequence of three consecutive letters is called a con. For example, in the preceding string, the cons are aac, gtt, tgt, aac, and cag. If we ignored the rst letter and started listing the cons starting at the second a, the cons would be acg, ttt, gta, and acc, and we would ignore the last ag. The letters are called bases. A DNA string can be hundreds of thousands of cons long, even millions of cons long, which means that it is infeasible to count them by hand. It would be useful to have a simple script that could count the number of occurrences of a specic con in such a string. For instance, for the example string above such a script would tell us that aac occurs three times and tgt occurs once. More generally, we want to be able to nd occurrences of arbitrary sequences of bases in a given DNA string, such as how many times ttatg occurs, or how many times cgacgattag occurs. Your job is to write a script named countmatches that expects at least two arguments on the command line. The rst argument is the pathname of a le containing a valid DNA string with no newline characters or white space characters of any kind within it. (It will be terminated with a newline character.) This le contains nothing but a sequence of the letters a, c, g, and t. The remaining arguments are strings containing only the bases a, c, g, and t in any order. For each valid argument string, it will search the DNA string in the le and count how many non-overlapping occurrences of that argument string are in the DNA string. To make sure you understand what non-overlapping means, the string ata occurs just once in the string atata, not twice, because the two occurrences overlap. If your script is called correctly, it will output for each argument a line containing the argument string followed by how many times it occurs in the string. If it nds no occurrences, it should output 0 as a count. For example, if the string aaccgtttgtaaccggaac is in a le named dnafile, then your script should work like this: $ countmatches dnafile ttt ttt 1 $ countmatches dnafile aac ggg aaccg 4

5 aac 3 ggg 0 aaccg 2 Warning: if it is given valid arguments, the script is not to output anything except the strings and their associated counts. No fancy messages, no words! The script should check that the rst argument is a le name and that there is at least one other argument after it. If the rst is not a le name or if it is missing anything after the lename, the script should print a how-to-use-me message and then exit. It is not required to check that the le is in the proper form, or that the string contains nothing but the letters a, c, g, and t. Hint: You can solve this problem using grep and one other command that appears in this cument. Although there are other lters, you not need them to solve this problem. You have to read more about grep to know how to use it. The other command has appeared in the slides already. Grading Rubric This homework is graded on a 100 point scale. Each script is worth 50 points. Each script will be graded on its correctness foremost. This means that it es exactly what the assignment states it must, in detail. Correctness is worth 70% of the grade. Then it is graded on its clarity, simplicity, and eciency, as described above. These qualitative measures are worth 30% of the grade. Submitting the Homework This assignment is due by the end of the day (i.e. 11:59PM, EST) on Thursday, September 28, You will submit it by putting it into a particular directory in our le system. In particular, there is a directory in the CSci Department network whose full path name is /data/biocs/b/student.accounts/cs132/projects/project2. To submit your project, you must follow the instructions below exactly! Do not deviate from these instructions. To be precise: 1. Login using ssh to eniac.cs.hunter.cuny.edu with your valid username and password, and then ssh into any cslab host. 2. In your own home directory, create a directory named project2_username, where username is your username on our system. 3. Put copies of the two scripts that you have written into this directory. Make sure they are named logincount and countmatches. 4. Run the command zip -r project2_username.zip project2_username where username is replaced by your username. This will create the le project2_username.zip. 5. Run the command /data/biocs/b/student.accounts/cs132/bin/submitproject 2 project2_username.zip 5

6 Do exactly this, of course with your real username in place of the placeholder username. Do not mistype it. The command will create a copy of the le project2_username.zip in the directory /data/biocs/b/student.accounts/cs132/projects/project2 It will be named project2_username, where username is your username on the network. You will not be able to read this le, nor will anyone else except for me. If you decide to make any changes and resubmit, just run the command again and it will replace the old le with the new one. I will be able to unzip the le, extracting whatever les you created. Do not try to put your le into this directory in any other way - you will be unable to this. Although these instructions may seem complicated, they simplify the way you submit your work and the way I can retrieve it. If you make mistakes, just start over. If things n't seem to work out, post a question on Piazza with the details included. 6