410 2.1 Command Line Bi 410/510: Command Line Interface Links 1 Overview 1.1 covered in Ch 4 and 5 of PCFB 1.2 no project 1.3 suggested exercises to help you get familiar with commands 2 History history.p… 3 File Hierarchy 3.1 in Unix terminology, a folder is called a directory 3.2 directories can contain files of any type or subdirectories 3.3 the top level folder is called the root directory 3.4 download, unpack a file named greeks.tgz [open greeks in Finder] a folder with seven subfolders and a text file use it to practice shell commands 4 Paths 4.1 a string that specifies a set of nested folders is a path 4.2 examples greeks/delta/diogenes.txt greeks/alpha/images/photos.tgz 4.3 the / character between folder names is the separator character Windows uses a backslash (\) Linux and Mac OS X are derived from Unix, use the forward slash (/) 5 Terminal Window 5.1 shell [open Terminal, go to documents] prompt enter command, hit return example: ls (“list the contents of a folder”) 5.2 shell commands first word is name of program to run lots are built in (ls, cd, wc, etc) others are names of applications (python, etc) 5.3 cd / ls first commands to learn: cd (“change directory”) and ls (“list directory”) [dir in Windows] all commands are run from a specific folder, called the “current directory” ** locate where you saved the greeks folder, see if you can use cd commands to navigate to that folder ** type the ls command to show you the contents of the folder 5.4 arguments additional words typed on command line are often file names or other arguments examples: ls greeks ls greeks/delta greeks/epsilon these words are passed to the program as an “argument vector” 5.5 options by convention, arguments that start with a dash are options example: ls -l, ls -a 5 Terminal Window 5.1 shell [open Terminal, go to documents] prompt enter command, hit return example: ls (“list the contents of a folder”) 5.2 shell commands first word is name of program to run lots are built in (ls, cd, wc, etc) others are names of applications (python, etc) 5.3 cd / ls first commands to learn: cd (“change directory”) and ls (“list directory”) [dir in Windows] all commands are run from a specific folder, called the “current directory” **Bi locate 410/510: where you savedCommand the greeks folder, Line see Interface if you can use cd commands to navigate to that folder Links ** type the ls command to show you the contents of the folder 5.4 arguments additional words typed on command line are often file names or other arguments examples: ls greeks ls greeks/delta greeks/epsilon these words are passed to the program as an “argument vector” 5.5 options by convention, arguments that start with a dash are options example: ls -l, ls -a 6 Navigation 6.1 working directory (where commands are executed) 6.2 pwd (print working directory) 6.3 special arguments: . and .. 7 Printing the Contents of a File 7.1 cat 7.2 more 8 Searching 8.1 grep 8.2 egrep 9 Miscellaneous 9.1 echo 9.2 wc (word count) 9.3 head and tail 10 Redirection 10.1 Use > to save output to a file echo “hello, world” echo “hello, world” > hello.txt 11 Pipes 11.1 the “pipe” symbol connect the output of one command as the input to another command 11.2 example: how many reference entries are at the start of the Genbank file? [sasquatch:downloads] ➤ grep REF NC_000913.prefix.txt ... REFERENCE 15 (bases 1 to 4639675) COMMENT PROVISIONAL REFSEQ: This record has not yet been subject to final RKKIRNEQRFASLDELKAQIARDELTAREFFGLTKPA" ... [sasquatch:downloads] ➤ egrep '^REF' NC_000913.prefix.txt REFERENCE 1 (bases 1 to 4639675) REFERENCE 2 (bases 1 to 4639675) REFERENCE 3 (bases 1 to 4639675) ... [sasquatch:downloads] ➤ egrep '^REF' NC_000913.prefix.txt | wc 15 90 540.