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Unix Master
This document is about Unix commands for bioinformaticians. It discusses Unix folders and files, processes, and redirection. It provides examples of commands for listing, moving, copying, reading and editing files. It also demonstrates running processes, controlling processes, and redirecting inputs/outputs. The goal is to introduce basic Unix skills like navigating the filesystem, working with files, and running programs needed for bioinformatics tasks.
Unix Master
- 1. Unix for BioinformaticiansA survival guide Paolo Marcatili - Programmazione 08-09
- 2. Agenda Unix FoldersFiles Processes Redirection Paolo Marcatili - Programmazione 08-09
- 3. Unix He cansmell your fear Paolo Marcatili - Programmazione 08-09
- 4. What is Unix ? Unix Paolo Marcatili - Programmazione 08-09
- 5. What is Unix ? Unix Paolo Marcatili - Programmazione 08-09
- 6. What is Unix ? Unix Paolo Marcatili - Programmazione 08-09
- 7. What is Unix ? Unix Paolo Marcatili - Programmazione 08-09
- 8. What is Unix ? Operating system stable, multi-user, multi-tasking for servers, desktops and laptops. Unix Paolo Marcatili - Programmazione 08-09
- 9. Types of UnixSolaris OS-X Linux! Unix Paolo Marcatili - Programmazione 08-09
- 10. Unix Operating SystemUnix Paolo Marcatili - Programmazione 08-09
- 11. What’s in Unix?Files Processes Unix Paolo Marcatili - Programmazione 08-09
- 12. Unix Filesystem UnixPaolo Marcatili - Programmazione 08-09
- 13. Terminal It makesthe difference! Powerful Transparent User-unfriendly Unix Paolo Marcatili - Programmazione 08-09
- 14. Our Task TodayYes, I can! Paolo Marcatili - Programmazione 08-09
- 15. Human Immunoglobulins TaskPaolo Marcatili - Programmazione 08-09
- 16. Human Immunoglobulins TaskPaolo Marcatili - Programmazione 08-09
- 17. The data Wehave 3 files Fasta Sequences of Heavy (heavy.fasta) Lambda (lambda.fasta) Kappa (kappa.fasta) Task Paolo Marcatili - Programmazione 08-09
- 18. The Task Lookdata Correct errors Do some analysis Make a single fasta file Task Paolo Marcatili - Programmazione 08-09
- 19. Folders: read andwrite Paolo Marcatili - Programmazione 08-09
- 20. Change Directory Toknow where you are >pwd /home/bioinfoSMFN Let’s move! >cd /home/bioinfoSMFN/Desktop/task Or >cd Desktop/ Folders Paolo Marcatili - Programmazione 08-09
- 21. Folder content Let’scheck what’s in the folder: >ls Better >ls -la Cheat: parameters are useful! >ls -lart Folders Paolo Marcatili - Programmazione 08-09
- 22. Wildcards Extremely useful!>ls -la *heavy* >ls -la heavy.?asta *= 0,1,2,…. occurences of whatever ?= exactly 1 occurence of whatever Folders Paolo Marcatili - Programmazione 08-09
- 23. Commands To knowmore about a command: >man ls >whatis ls >apropos ls Or Google! Folders Paolo Marcatili - Programmazione 08-09
- 24. Unix Permissions FoldersPaolo Marcatili - Programmazione 08-09
- 25. Folders - summaryCommand Meaning ls list files and directories ls -a list all files and directories mkdir make a directory cd directory change to named directory cd change to home-directory cd ~ change to home-directory cd .. change to parent directory pwd path of the current directory Folders Paolo Marcatili - Programmazione 08-09
- 26. Files: read andwrite Paolo Marcatili - Programmazione 08-09
- 27. Backup original dataCreate a directory >mkdir backup Copy all the files in the directory >cp heavy.fasta backup/ >cp heavy.fasta heavy_copy.fasta >mv heavy_copy.fasta backup/heavy_backup.fasta Files Paolo Marcatili - Programmazione 08-09
- 28. Read a fileLet’s see… >cat heavy.fasta Files Paolo Marcatili - Programmazione 08-09
- 29. Read a fileLet’s see… >cat heavy.fasta Mmh… >less heavy.fasta Hint: q to quit… but if you are stuck try ctrl+c Files Paolo Marcatili - Programmazione 08-09
- 30. Look for textIf we want to look for something while in less: / 91979410 (enter) Files Paolo Marcatili - Programmazione 08-09
- 31. Edit a fileLet’s remove the first H sequence >vi heavy.fasta >nano heavy.fasta For those who live in 2008 >gedit heavy.fasta Files Paolo Marcatili - Programmazione 08-09
- 32. Look for textHow many Igs in each file? We can count the lines! >wc heavy.fasta Files Paolo Marcatili - Programmazione 08-09
- 33. Look for textHow many Igs in each file? We can count the lines! >wc heavy.fasta Lines > proteins!!! Files Paolo Marcatili - Programmazione 08-09
- 34. Grep # ofproteins = # of “>” in a file >grep “>” heavy.fasta >grep -c “>” heavy.fasta Do it for all the files and write the result (I think they are too many…) Files Paolo Marcatili - Programmazione 08-09
- 35. Grep >grep -cV-region heavy.fasta >grep -c v-region heavy.fasta >grep -ci v-region heavy.fasta Ok, better! Files Paolo Marcatili - Programmazione 08-09
- 36. Files: sumary cpfile1 file2 copy file1 and call it file2 mv file1 file2 move or rename file1 to file2 rm file remove a file cat file display a file less file display a file a page at a time head file display the first few lines tail file display the last few lines grep 'key' file search a file for keywords wc file number of lines Files Paolo Marcatili - Programmazione 08-09
- 37. Processes Paolo Marcatili- Programmazione 08-09
- 38. Run a processProcess = execution of some instructions Usually the instructions are in a file. e.g. less -> /usr/bin/less So >/usr/bin/less heavy.fasta Processes Paolo Marcatili - Programmazione 08-09
- 39. Run - It’ssimple Ok, so let’s try >./loop.pl Processes Paolo Marcatili - Programmazione 08-09
- 40. Run - It’ssimple Ok, so let’s try >./loop.pl Ok, and now? Processes Paolo Marcatili - Programmazione 08-09
- 41. Controlling processes Ctrl+z -> go to sleep Now you’ve got the control again! But it’s not still dead… bg Ctrl+C Processes Paolo Marcatili - Programmazione 08-09
- 42. Controlling processes Or:>./loop.pl Ctrl+z >ps >top ( q to exit) >kill the_number_that_you_have_just_read Processes Paolo Marcatili - Programmazione 08-09
- 43. Redirection Control theforce Paolo Marcatili - Programmazione 08-09
- 44. Inputs and outputsKeyboard Mouse Tablet Kernel Display Printer File Redirection Paolo Marcatili - Programmazione 08-09
- 45. Write into afile >Cat > lista.txt Heavy 29061 Ctrl+d And >less lista.txt Redirection Paolo Marcatili - Programmazione 08-09
- 46. Append to afile >Cat >> lista.txt Kappa 7476 Ctrl+d And >less lista.txt Redirection Paolo Marcatili - Programmazione 08-09
- 47. The big one!>cat heavy.fasta > bigone.fasta >cat kappa >> bigone.fasta >cat lambda.fasta >> bigone.fasta >grep -c “>” bigone.fasta Redirection Paolo Marcatili - Programmazione 08-09
- 48. Extract headers >grep“>” bigone.fasta > headers.head >sort headers.head > headers_sort.head Do we need the first file? Redirection Paolo Marcatili - Programmazione 08-09
- 49. Extract headers >grep“>” bigone.fasta > headers.head >sort headers.head > headers_sort.head Do we need the first file? No! >grep “>” bigone.fasta | sort > headers_sorted.head | is called pipe, and it’s something Redirection Paolo Marcatili - Programmazione 08-09
- 50. Redirect everything! >grep">" biggone.fasta 2> err.log >less err.log Redirection Paolo Marcatili - Programmazione 08-09
- 51. Redirect - summarycommand > file redirect std output to a file command >> file append std output to a file command < file redirect std input from a file cmd1 | cmd2 pipe the output of cmd1 to the input of cmd2 cat f1 f2 > f0 concatenate f1 and f2 to f0 sort sort data Redirection Paolo Marcatili - Programmazione 08-09
- 52. Quiz What doesthis command perform? >grep -v ">" heavy.fasta How many proteins in each file? How many residues in each file? (hint: wc -m counts the # of char in a line) Average length of proteins in each file? Average content of Prolines of VH, VL and VK? (hint: look at grep parameters) Paolo Marcatili - Programmazione 08-09