The Unix Shell. Pipes and Filters

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1 The Unix Shell Copyright Software Carpentry 2010 This work is licensed under the Creative Commons Attribution License See for more information.

2 shell

3 shell pwd mkdir cd nano ls rm. rmdir.. mv cp

4 shell pwd mkdir cd nano ls rm. rmdir.. mv cp More powerful when combined

5 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $

6 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $

7 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb

8 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb * is a wild card

9 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb * is a wild card matches zero or more characters

10 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb * is a wild card matches zero or more characters so *.pdb matches all filenames ending in.pdb

11 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb wc cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb

12 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb word count

13 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb word count counts lines, words, and characters in files

14 $ ls molecules cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb $ cd molecules $ wc *.pdb $ cubane.pdb ethane.pdb methane.pdb octane.pdb pentane.pdb propane.pdb total

15 $ wc -l *.pdb 20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total $ report only lines

16 $ wc -l *.pdb 20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total $ report only lines use -w for words or -c for characters

17 20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total Which file is shortest?

18 20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total Which file is shortest? Easy to see when there are six

19 20 cubane.pdb 12 ethane.pdb 9 methane.pdb Which file is shortest? Easy to see when there are six 30 octane.pdb but what if there were 6000? 21 pentane.pdb 15 propane.pdb 107 total

20 $ wc -l *.pdb > lengths $

21 $ wc -l *.pdb > lengths $ redirect output to a file

22 $ wc -l *.pdb > lengths $ redirect output to a file create file if it doesn't exist

23 $ wc -l *.pdb > lengths $ redirect output to a file create file if it doesn't exist overwrite it if it does

24 $ wc -l *.pdb > lengths $ no screen output

25 $ wc -l *.pdb > lengths $ ls lengths lengths $

26 $ wc -l *.pdb > lengths $ ls lengths lengths $ cat lengths $ 20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total

27 $ wc -l *.pdb > lengths $ ls lengths lengths $ cat lengths concatenate files 20 cubane.pdb 12 ethane.pdb 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total $

28 $ wc -l *.pdb > lengths $ ls lengths lengths $ cat lengths concatenate files 20 cubane.pdb in this case, only one 12 ethane.pdb so file contents printed to screen 9 methane.pdb 30 octane.pdb 21 pentane.pdb 15 propane.pdb 107 total $

29 $ sort lengths 9 methane.pdb 12 ethane.pdb 15 propane.pdb 20 cubane.pdb 21 pentane.pdb 30 octane.pdb 107 total $

30 $ sort lengths > sorted-lengths $

31 $ sort lengths > sorted-lengths $ head -1 sorted-lengths 9 methane.pdb $

32 $ sort lengths > sorted-lengths $ head -1 sorted-lengths 9 methane.pdb get the first line of the file $

33 $ sort lengths > sorted-lengths $ head -1 sorted-lengths 9 methane.pdb get the first line of the file $ this must be the PDB file with the fewest lines, since sorted-lengths holds files and line counts in order from least to greatest

34 $ sort lengths > sorted-lengths $ head -1 sorted-lengths 9 methane.pdb get the first line of the file $ this must be the PDB file with the fewest lines, not particularly obvious since sorted-lengths holds files and line counts in order from least to greatest

35 $ sort lengths head -1 $ 9 methane.pdb

36 $ sort lengths head -1 $ 9 methane.pdb a pipe

37 $ sort lengths head -1 $ 9 methane.pdb a pipe use output of left side

38 $ sort lengths head -1 $ 9 methane.pdb a pipe use output of left side as input to right side

39 $ sort lengths head -1 $ 9 methane.pdb a pipe use output of left side as input to right side without creating temporary file

40 $ wc -l *.pdb sort head -1 9 methane.pdb $ don't need to create lengths file

41 $ wc -l *.pdb sort head -1 $ 9 methane.pdb This simple idea is why Unix has been so successful

42 $ wc -l *.pdb sort head -1 $ 9 methane.pdb This simple idea is why Unix has been so successful Create simple tools that:

43 $ wc -l *.pdb sort head -1 $ 9 methane.pdb This simple idea is why Unix has been so successful Create simple tools that: do one job well

44 $ wc -l *.pdb sort head -1 $ 9 methane.pdb This simple idea is why Unix has been so successful Create simple tools that: do one job well work well with each other

45 $ wc -l *.pdb sort head -1 $ 9 methane.pdb This simple idea is why Unix has been so successful Create simple tools that: do one job well work well with each other 10 tools can be combined in 100 ways

46 running program

47 running program process

48 standard input

49 standard input stdin

50 standard output stdout

51 shell

52 $ wc -l *.pdb > lengths

53 wc $ wc -l *.pdb > lengths

54 wc $ wc -l *.pdb > lengths

55 wc lengths $ wc l *.pdb > lengths

56 wc sort $ wc l *.pdb sort

57 wc sort head -1 $ wc l *.pdb sort head -1

58 This programming model called pipes and filters

59 This programming model called pipes and filters A filter transforms a stream of input into a stream of output

60 This programming model called pipes and filters A filter transforms a stream of input into a stream of output A pipe connects two filters

61 This programming model called pipes and filters A filter transforms a stream of input into a stream of output A pipe connects two filters Any program that reads lines of text from standard input, and writes lines of text to standard output, can work with every other

62 This programming model called pipes and filters A filter transforms a stream of input into a stream of output A pipe connects two filters Any program that reads lines of text from standard input, and writes lines of text to standard output, can work with every other You can (and should) write such programs

63 pwd mkdir cd nano ls rm. rmdir.. mv cp

64 pwd mkdir wc cd nano sort ls rm head. rmdir.. mv cp

65 pwd mkdir wc cd nano sort ls rm head. rmdir tail.. mv split cp cut uniq

66 pwd mkdir wc * cd nano sort > ls rm head. rmdir tail.. mv split cp cut uniq

67 pwd mkdir wc * cd nano sort > ls rm head. rmdir tail <.. mv split? cp cut uniq

68 created by Greg Wilson August 2010 Copyright Software Carpentry 2010 This work is licensed under the Creative Commons Attribution License See for more information.

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