YXF-biostar 基本命令

Example in this note： home/yxf/edu/lecture

The Unix bootcamp

1. ls: list of files and directories in home directories
2. pwd: Which directory you are working at
3. mkdir: make new directory
   mkdir edu
4. cd: change directory A to directory B.
   cd edu----change current directory to edu directory
5. Back to home: cd / (cd /, cd ~ is same)
   cd home
   cd yxf
   or: cd /home/yxf
6. cd .. : Navigate upward directory
   cd edu
   pwd: /home/yxf/edu
   cd ..
   pwd: /home/yxf
7. Absolute path: No /
   Relative path:
8. manual command: man ls
   man cd
   man man
9. rm: remove directories
   rm ~/edu/lecture/
   rmdir data
   cd ..
   rmdir lecture
10. touch: creat new empty file
    cd edu
    touch heaven.txt
    touch earth .txt
    ls
11. mv(1): move file
    mkdir temp
    mv heaven.txt temp
    mv earth.txt temp
    ls temp
12. mv(2): remame file (another function)
    tough rags
    ls
    mv rags temp/riches
    ls temp
13. mv(3): move directories
    mv temp temp2
    ls temp2
14. rm: remove file
    cd templs
    rm -i earth.txt heaven.txt rags (Function of "i" command-line option is to ask for confirmation)
15. cp: copy files
    touch file1
    cp file1 file2 ---in same directory
    ls
    touch ~/edu/file3
    cp ~edu/file3 ~/edu/lecture/
16. echo: put text in a file and view it
    ecoh "call me king"
    call me king
    ecoh "call me king" > oening_line.txt
    ls
    more opening_line.txt-----view content of file
17. cat: combine multiple files
    echo "the primroses were over." >> opening_line.txt
    cat opening_line.txt

Data analysis

1. Download data online (file name is "SGD_features.tab")
   At first make a new directory (lec03) and then download data in new directory
2. View data
   more SGD_features.README
3. Open stream from data
   cat SGD_features.tab
4. Check how many lines in the file
   cat SGD_features.tab | wc -l
   "cat SGD_features.tab | wc" or "wc -l SGD_features.tab" will check the number of lines, words and characters
5. Search desired data:
   grep: which lines match a certain pattern
   cat SGD_features.tab | grep YAL060W ----Find information on gene YAL060W
   cat SGD_features.tab | grep YAL060W --color=always | head ----Highlight the matched pattern
6. Search data without a given pattern
   cat SGD_features.tab | grep -v Dubious | wc -l ---- the number of lines which not contain "Dubious"
7. Store result in a new file
   ">" character is redirection
   cat SGD_features.tab | grep YAL060W > match.tab
8. How to select gene
   "cut" is used to select certain colimn of gene
   cat SGD_features.tab | cut -f 2 | head ----select data of column 2
   cat SGD_features.tab | cut -f 2 | grep ORF | wc -l ----how many ORF gene
   cat SGD_features.tab | cut -f 2,3,4 | grep ORF | head ----select multiple columns
9. How many feature types are in this data
   Make a new file for this feature type(ORF): cat SGD_features.tab | cut -f 2 > types.txt
   ?sorting
   ?unique

Compressed files and directories

1. Compressed format
   Single file : .gz, .bz, .bz2, .zip
   Multiple files: .tar.gz, .tar.bz2
2. How to compress or uncompress a file
   data: AF086833.fa
   compress: gzip AF086833
   uncompress: gunzip AF086833.fa.gz
3. How to compress or uncompress multiple files
   data: AF086833.fa, AF086833.gb
   Compress format: tar czfv archive-name list-of-files-that-go-into-the-archive
   czfv: creat a compressed file in verbose mode
   tar czfv sequences.tar.gz AF086833.fa AF086833.gb
   Or: tar czvf sequences.tar.gz AF086833.*
   Better way: mkdir sequences
   mv AF086833.* aequences/
   tar czvf sequences.tar.gz sequences/*

管道命令：就是多个命令联用，上一个命令的输出是下一个命令的输入。通俗来讲就是命令A的数据结果就是命令B的输入数据，两个命令之间以管道符“|”连接