Don't forget grep

I've always had a hard time with text processing in R. (Of course, with RPy, I don't need to worry about this so much anymore). Still, it's important to remember the R function grep; the basic usage is:

grep(pattern, x)

Here's a very simple example:

names = paste(rep(c('A','B'),3),1:6,sep='') > names [1] "A1" "B2" "A3" "B4" "A5" "B6" > sel = grep('B',names) > sel [1] 2 4 6 > colors = rep('red',length(names)) > colors[sel] = 'blue' > colors [1] "red" "blue" "red" "blue" "red" "blue"

We might use this in ape to color the labels for the tips of a tree depending on the origin of the sequence (say, database or patient sample).

In Python, you'd probably do something like this:

>>> L = list('AB')*3 >>> L = [item + str(i+1) for i,item in enumerate(L)] >>> L ['A1', 'B2', 'A3', 'B4', 'A5', 'B6'] >>> cL = ['red'] * len(L) >>> for i,n in enumerate(L): ... if 'B' in n: ... cL[i] = 'blue' ... >>> cL ['red', 'blue', 'red', 'blue', 'red', 'blue']