Principles of Bioinformatics. BIO540/STA569/CSI660 Fall 2010

Transcription

1 Principles of Bioinformatics BIO540/STA569/CSI660 Fall 2010

2 Lecture Five Practical Computing Skills

3 Emphasis This time it s concrete, not abstract. Fall 2010 BIO540/STA569/CSI660 3

4 Administrivia Monday s class will be a lab. Nothing to do to prepare, except to show up. Fall 2010 BIO540/STA569/CSI660 4

5 Files There are many different Operating Systems Since it s used in much scientific work, we ll concentrate on the Unix operating system. Similar to Linux, Mac OS X s terminal environment. Fall 2010 BIO540/STA569/CSI660 5

6 Files Information is organized in files Fall 2010 BIO540/STA569/CSI660 6

7 Unix Filesystem As with most operating systems, files in Unix are structured as a hierarchically organized set of Folders (Directories) - areas in the filesystem that can hold files, as well as other folders, Files Fall 2010 BIO540/STA569/CSI660 7

8 Unix Filesystem Root - the top of the filesystem. While not strictly a tree, that is how filesystems are typically viewed. They can have cycles, using aliases. Fall 2010 BIO540/STA569/CSI660 8

9 Unix Filesystem Current working directory - the directory/- folder that you are currently using. When you first log in, your current working directory is your home directory The home directory is a special directory associated with your account. Fall 2010 BIO540/STA569/CSI660 9

10 Unix Filesystem Paths - how to specify where in the filesystem something is. Absolute path - the entire path Relative path - just the portion of the path relative to your current location.. - your current directory.. - the directory above your current directory. Fall 2010 BIO540/STA569/CSI660 10

11 How to log on Type ssh cifalab.ss.albany.edu -l youruserid or ssh Then give (your userid if asked) and your password. You will then be at the shell (terminal) prompt. Fall 2010 BIO540/STA569/CSI660 11

12 How to log on Or telnet cifalab.ss.albany.edu if you don't have ssh client access. But, telnet does not cryptographically protect your password or commands to the computer like ssh does. Fall 2010 BIO540/STA569/CSI660 12

13 How to log off Type exit and hit the return key. Fall 2010 BIO540/STA569/CSI660 13

14 Unix Commands Command Line As opposed to Graphic User Interface (GUI) or Web Interface. Fall 2010 BIO540/STA569/CSI660 14

15 Command Format Unix commands are of the form command -options -options arguments Fall 2010 BIO540/STA569/CSI660 15

16 ls To get a detailed (long) listing of the files in your current working directory: ls -l Fall 2010 BIO540/STA569/CSI660 16

17 Copying Before modifying a file, you might want to make a copy of it. The command is cp originalfilename newfilename Fall 2010 BIO540/STA569/CSI660 17

18 Copying If you want to be extra sure of your copy, you can set the permissions so that you cannot change or delete it. chmod -w file1 This will prohibit anyone from changing (Writing) file file1. Including you. Fall 2010 BIO540/STA569/CSI660 18

19 More The command more filename displays the file filename a screenful at a time. Fall 2010 BIO540/STA569/CSI660 19

20 Grep The grep command searches files for specified data. For instance, the command grep foo file2 searches for instances of foo in the file file2. Fall 2010 BIO540/STA569/CSI660 20

21 grep The command grep "HUMAN" bulkall_if.txt extracts only the sequences data containing the word human. Note that HUMAN is in all upper case letters. This is exactly what will match, not Human, human, etc. Fall 2010 BIO540/STA569/CSI660 21

22 grep The command grep -w PDB fn searches for only the word PDB in the file fn. By word it means that it won t find PDB if it s part of a larger word. For example NonPDBinformation Fall 2010 BIO540/STA569/CSI660 22

23 grep The command grep "HUMAN" bulkall_if.txt grep -w PDB is a pipelined, multistage search. First it does a grep for HUMAN, and then does a further grep on PDB on those lines containing HUMAN. The -w argument means search only for entire words that match. As opposed to words that are parts of larger words. Fall 2010 BIO540/STA569/CSI660 23

24 Grep There are a lot of variations to commands. For example, grep -c ^ID uniprot_sprot.dat The ^ limits it to the beginning of the line, and the -c gives a count, not the data itself. A similar command: grep -c ^\/\/ uniprot_sprot.dat Fall 2010 BIO540/STA569/CSI660 24

25 Egrep The egrep command allows multiple patterns egrep "^ID SUBCELLULAR" uniprot_sprot.dat more Fall 2010 BIO540/STA569/CSI660 25

26 Egrep The command egrep "^ID ^ " fn extracts lines starting with ID or that start with a blank. Fall 2010 BIO540/STA569/CSI660 26

27 Pipelines and streams Input Output Streams Fall 2010 BIO540/STA569/CSI660 27

28 Pipelines and streams Input Output Fall 2010 BIO540/STA569/CSI660 28

29 Pipelines and streams Input Output Fall 2010 BIO540/STA569/CSI660 29

30 Pipelines and streams Input Output Fall 2010 BIO540/STA569/CSI660 30

31 Creating files with extracted (field) data. Redirect the output of a command to a file. Fall 2010 BIO540/STA569/CSI660 31

32 Cut The cut command extracts data from a file. For example cut -f 1,3 interested in only first and third fields. The cut command indexes (counts) its fields starting with 1, not 0. Fall 2010 BIO540/STA569/CSI660 32

33 More Cut For the command cut -d' ' -f2,4 the delimiter is the character ' ' and we're interested in fields 2 and 4 Fall 2010 BIO540/STA569/CSI660 33

34 Fields Commands like cut can use both Fixed length fields, and varying length fields (delimited). Fall 2010 BIO540/STA569/CSI660 34

35 Filename wildcards You can specify multiple files using filename wildcards. For example, the command grep -c \> *.aa looks for instances of > in any file with a name that ends in.aa Fall 2010 BIO540/STA569/CSI660 35

36 wc wc combined with grep for doing counts. The wc program gives totals. The command grep HUMAN fn wc -l first finds all lines containing the string HUMAN and then counts the number of those lines. Fall 2010 BIO540/STA569/CSI660 36

37 Wrapping v. Truncating Lines that are wrapped in a display. Wrapping v. truncating. Fall 2010 BIO540/STA569/CSI660 37

38 Resources There are many online tutorials on different aspects of Unix. Google Unix tutorial and find some that suit you. Fall 2010 BIO540/STA569/CSI660 38