Here you will find the instruction materials for the first week of class.
Lecture slides for Week One:
Cheat Sheet of commands:
If you are a Google Drive user, the links are as follows:
For our bonus exercise, here are your files:
The instructions are as follows:
Copy all the tree files to home
Remove all the tree file in home
Concatenate all the tree files in a file called trees.txt in home
How many trees are in this file?
The second tree is unrooted and has node labels. Make a new file with just the second tree from each of the tree files called trees2.txt
The answers are as follows (highlight to view):
Copy all the tree files to home (cp tree*/tree*.txt .)
Remove all the tree file in home (rm tree*.txt)
Concatenate all the tree files in a file called trees.txt in home (cat tree*/tree*.txt >> trees.txt)
How many trees are in this file? (grep ";" trees.txt | wc -l)
The second tree is unrooted and has node labels. Make a new file with just the second tree from each of the tree files called trees2.txt (tail -n 1 tree*/tree*.txt >> trees2)
FAQ from class today:
“How do I get out of man?”
-Get out of man by typing q
“When I’m using wildcard, is Unix case sensitive?”
-Unix is case-sensitive
“Where is pipe?”
-The pipe | symbol is found above your enter/return key. Hold down shift while pressing this key to get the pipe.
“Can we use grep to exclude lines? Like, print every line that does not have that text?”
-The -v flag gets every line except the grep text
“How can I rename a file?”
-mv file1 file2 will move file1 to be file2. file1 will no longer exist, and you will only have file2.
Also, if you'd like to learn a little more about programming, here are some recommended resources:
- Book: Practical Computing for Biologists by Haddock and Dunn** Excellent for beginners
- Book: Bioinformatics Programming in Python by O'Reilly Books** Very good methods
- http://greenteapress.com/thinkpython/thinkpython.pdf** Free e-book on thinking like a programmer and using Python
- CodeAcademy.com** Live-feedback exercises to practice Python
- http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.0030199** PLoS Primers are a great source of free info on many topics, including this one on programming for non-computer scientists"Practical Computing for Biologists" (Haddock and Dunn)
