University:
Boston University
Course:
MET CS 201 | Introduction to Programming
Academic year:

2023
Views:

49

Pages:

17
Author:

Jarrett Richard

Variables Environment Variables ● Contain environment configuration ○ Typically for the shell, but other programs can set their own. ● Created automatically when logged in. ● Scope is global ○ Other programs can read/use them to know how to behave. ● Type “env” to see the full list. scc1 $ echo $USER cjahnke scc1 $ echo $PWD /usr3/bustaff/cjahnke scc1 $ echo $HOSTNAME scc1 scc1 $ env MODULE_VERSION_STACK=3.2.10 XDG_SESSION_ID=c8601 HOSTNAME=scc1 TERM=xterm SHELL=/bin/bash HISTSIZE=1000 TMPDIR=/scratch SSH_CLIENT=128.197.161.56 55982 22 ... Shell Variables ● A character string to which a user assigns a value. ● Not real data, but could point to data (lists, file, device, etc) ● Shell variables have limited scope ○ only current shell ● Can create, assign, and delete. scc1 $ myvar=foo scc1 $ echo $myvar foo scc1 $ myvar=bar scc1 $ echo $myvar bar scc1 $ unset myvar scc1 $ echo $myvar scc1 $ scc1 $ myvar=foo scc1 $ bash scc1 $ echo $myvar scc1 $ exit exit scc1 $ echo $myvar foo Choosing a Variable Name and Style Variable names cannot have spaces. Pick and try to stick to a style. ● CAPITALS ○ Environment variables and OS shell variables are usually capitalized. ● lowercase ○ Effective for simple scripts, hard to read if names are complicated (e.g. $mynewvar). ● Under_scores ○ Common alternative to spaces (e.g. $my_new_var). Bash does not accept hyphens. ● camelCase ○ Capitalization patterns are concise and easy enough to read (e.g $myNewVar). Using variables: The dollar sign and quotes ● No quote ○ Simple. Bash shell interprets variable ● Escape Special Character (“\”) ○ The “$” is special and indicates a variable in Bash. The “\” escapes special behavior and instructs bash to treat it as a character. ● Single Quote ○ Literal. Exactly the contents. scc1 $ hi=Hello scc1 $ echo $hi Hello scc1 $ echo \$hi $hi scc1 $ echo '$hi' $hi ● Double Quote ○ Interpreted. Allows variable expansion. scc1 $ echo "$hi" Hello Using Variables: Strings, spaces, and quotes scc1 $ hello0=Hello World -bash: World: command not found scc1 $ echo $hello0 Hello Spaces are special too ● We can escape (“\”) the special behavior ● Or we can quote the string. ○ Single or double quotes are effectively the same if there is nothing to be interpreted. scc1 $ hello1=Hello\ World scc1 $ echo $hello1 Hello World scc1 $ hello2='Hello World' scc1 $ echo $hello2 Hello World scc1 $ hello3="Hello World" scc1 $ echo $hello3 Hello World Build up simple script myscript.sh echo Hello World scc1 $ bash myscript.sh myScriptVar=bar echo “My working directory \$PWD prints $PWD” Hello World My working directory $PWD prints /usr3/bustaff/cjahnke/bash bar echo $myScriptVar scc1 $ echo $myScriptVar scc1 $ Handling Arguments Command-line Arguments in Bash The command used to start a bash script passes the command information to the script as variables when it runs. This information is accessed through numbered variables where the “#” is the index of the information. ● ● ● ● $0 → The script name $1 → The first argument following the script name $2 → The second argument following the script name ... Note: only 9 arguments are captured; after that, you need to be creative. Simple Command Line Argument Example cli_arg.sh Terminal #!/bin/bash scc1 $ # $0 echo # $1 echo # $2 echo scc1 $ ./cli_arg.sh arg1 “2 items” 3rd $0 is ./cli_arg.sh $1 is arg1 $2 is 2 items is the script itself '$0' is "$0" is the first argument '$1' is "$1" is the second argument '$2' is "$2" Standard I/O, Pipes, and Redirection Jumping into Standard I/O There are 3 standard methods of communicating with a program Name Standard In Shorthand Stdin Purpose * Stream ID Command line inputs 0 Standard Out Stdout Normal output 1 Standard Error Stderr Error or other information 2 * What they are actually used for is entirely dependent on the program TERMINAL written files Keyboard 0 Process 1 STDOUT 2 Display STDERR Standard Out & Standard Error scc1 $ scc1 $ man What manual page do you want? man Terminal stdout scc1 $ man 1> man.stdout 2> man.stderr scc1 $ cat man.stdout scc1 $ cat man.stderr What manual page do you want? stderr What manual page do you want? Pipes ● Pipes (“|”) redirect the standard output of a command to the standard input of another command. ● Example: [cjahnke@scc1 ~]$ cat sample.vcf cat sample.vcf #CHROM 3 2 1 3 6 POS 14370 17330 1110696 1230237 1234567 ID rs6054257 . rs6040355 . microsat1 REF G T A T GTCT | cut -f1,2,7 | ... ... ... ... ... ... | sort -k3 cut -f1,2,7 #CHROM 3 2 1 3 6 POS 14370 17330 1110696 1230237 1234567 FILTER PASS q10 PASS PASS PASS | sort -k3 #CHROM 1 3 3 6 2 POS 1110696 1230237 14370 1234567 17330 FILTER PASS PASS PASS PASS q10 Redirection ● The “>” symbol redirects the standard output (default) of a command to a file. Redirection Description COMMAND < filename Input - Directs a file COMMAND << stream Input - Directs a stream literal COMMAND <<< string Input - Directs a string COMMAND > filename Output - Writes output to file (will “clobber”) COMMAND >> filename Output - Appends output to file ● Example: [cjahnke@scc1 ~]$ cat sample.vcf | cut -f1,2,7 | sort -k3 > sorted.txt Many characters use or modify this behavior ● ● ● ● ● ● ● ● A < file B > file C >> file D 2> file E &> file F|G H |& K M | tee file Use the contents of file as input for A Create a new file and write the standard out of B there (overwrites) If file exists append standard out of C to file, if file does not exist create it Create a new file and write the standard err of D there Combined the standard error and standard out and write to file Use the standard out of F as the standard in of G Combine the standard out and err of H and use as the standard in of K Write the standard out of M to both the terminal and to file scc1 $ module -t avail |& tee allmodules | grep python