Note
Learning Goals:
Homework grading: Show work on laptops:
Directory structure from Fig. 1 of PLoS paper
Renamed yeast directory to human
Downloaded CHR_MT fasta file into human directory
Show number of lines in hs_alt_HuRef_chr21.fa
Do homework assignment to demonstrate: bash file completion
ls with -R
Overview of ftp, client server protocols: Transfer files with ftp: Walk through download of CHR_MT from NCBI.
View files, search for text in files: Use cat to send contents of file to screen.
Use less to look at contents of file.
Use / to find things with less
Use grep to find string in fasta file.
How many lines contain AAAAAAA?
Read grep man page to determine how to get just a count
Use / again in man page to find word ‘count’
Login to remote computer: ssh
Login to EC2 instance: ec2-23-20-18-242.compute-1.amazonaws.com
recreate msms directory from PLoS paper
log out, log back in
Intro to vi: vi vimtutor.txt
ESC :q to quit
Reading
Exercises
Edit a file with vi editor:
Login to EC2 instance: ec2-23-20-18-242.compute-1.amazonaws.com
copy the file /jscbio2710/vimtutor.txt
- open the file with vi: vi vimtutor.txt
Anytime the document refers to the command vimtutor it is the same as: vi vimtutor.txt
follow and complete all of Lesson 1 and Lesson 2
you can copy the file again from /jscbio2710/vimtutor.txt if you need to start over or just practice some more
Turn In
- Log in to ec2-23-20-18-242.compute-1.amazonaws.com and complete Lesson 1 and Lesson 2 of the vimtutor.txt document. Leave the file in your home directory.
- On the EC2 machine, copy the file /jscbio2710/holmes.txt to your home directory. Edit the file with vi and correct the various spelling mistakes or missing letters. Leave the file in your home directory.
- On the EC2 machine in your home directory use vi to create a new file named week-2-1.txt. In this file write a few sentences about what we have learned so far. Leave this file in your home directory.
- The three files mentioned above will be copied out of your home directory at 8:30am on Thursday morning, the latest homework can be turned in.
Sign up for an XSEDE account: At the bottom of the sign in box (“Enter the Portal”), below the SIGN IN button, there is a link to create an account. Use this link to create a new account. Send email to me (James.Vincent@jsc.edu ) when you have completed this. I will verify through XSEDE.
Note
Learning Goals:
What will be covered in class:
Homework grading
Quiz 2
Review of vi:
vi filename <ENTER> start vi <ESC> :q! <ENTER> quit without saving changes <ESC> :wq <ENTER> quit and save changes. <ESC> back to command mode <ESC> will cancel an unwanted and partially completed command. u undo last action U undo all changes to line move cursor: h (left) j (down) k (up) l (right) 0 start of line $ end of line gg start of file G end of file 4G 4th line in file 15G 15th line in file i insert text a append at next character A append at end of line x delete character dw delete word d$ delete to the end of line dd delete line repeat a motion, prepend with a number: 2w Examples: 5j move down 5 lines 3k move up three lines 23l move 23 characters right 32h move 32 characters left operator [number] motion operator - what to do, such as d for delete [number] - optional count to repeat the motion motion - moves over the text to operate on, such as w (word), $ (to the end of line), etc. p put a line c change characters ce change to end of word c$ change to end of line r replace character R replace until outShell scripts:
#!/bin/bash echo "Hello World" echo "Today is: "
- The echo, date commands
- Make a bash shell script
- Changing permissions on bash script to make it executable
- Running the script
- Introducing errors on purpose
- Using variables
Class Project
Reading
- http://www.ee.surrey.ac.uk/Teaching/Unix/unix3.html
- http://www.ee.surrey.ac.uk/Teaching/Unix/unix4.html
- http://www.ee.surrey.ac.uk/Teaching/Unix/unix5.html
- Metagenomics - Hugenholtz
- http://www.panix.com/~elflord/unix/bash-tute.html
Exercises
- Complete all exercises in the Unix Tutorial (parts 3,4,5) above.
- Make sure you can do the exercises quickly, repeat as needed
- Turn In
You will create three shell scripts on the AWS server. Leave them in a directory called homework within your home directory.
- Create a directory called homework in your home directory on the AWS server we have been using:
ec2-23-20-18-242.compute-1.amazonaws.com
Create a shell script call homework-3a.sh in your homework directory.
Make the script a bash shell script
Add commands to the script to recreate the directory structure from the PLoS paper Figure 1 given as homework last week (Week 1, Thursday homework).
Create another bash script called homework-3b.sh.
Add command to this script to list all the files in the /tmp directory and count how many files there are.
Add echo and date commands to create a nicely formatted output report that includes your name, the date, the purpose of this script and finally the output of the commands themselves.
Create a bash script called homework-3c.sh.
If you don’t already have it, retreive another copy of human chromosoe 21 from ftp.ncbi.nih.gov.
Write commands in your shell script to list the size of this file. Make sure the chromosome file is in the homework directory also.
Add commands to this script to count the number of lines that contain the string ‘AAAAAAAAAA’
Use a variable at the top of your script to hold the name of the chromosome fasta file. Use this variable in the commands above instead of the file name itself.
