bioinformatics

I'm trying to solve a Rosalind basic problem of counting nucleotides in a given sequence, and returning the results in a list. For those ones not familiar with bioinformatics it's just counting the number of occurrences of 4 different characters ('A','C','G','T') inside a string. I expected collections.Counter to be the fastest method (first because they claim to be high-performance, and second because I saw a lot of people using it for this specific problem). But to my surprise this method is the slowest ! I compared three different methods, using timeit and running two types of experiments:

I am trying to find a way to collapse rows with intersecting ranges, denoted by "start" and "stop" columns, and record the collapsed values into new columns. For example I have this data frame: my.df<- data.frame(chrom=c(1,1,1,1,14,16,16), name=c("a","b","c","d","e","f","g"), start=as.numeric(c(0,70001,70203,70060, 40004, 50000872, 50000872)), stop=as.numeric(c(71200,71200,80001,71051, 42004, 50000890, 51000952))) chrom name start stop 1 a 0 71200 1 b 70001 71200 1 c 70203 80001 1 d 70060 71051 14 e 40004 42004 16 f 50000872 50000890 16 g 50000872 51000952 And I am trying to find the

I have two data.frames each with three columns: chrom, start & stop, let's call them rangesA and rangesB. For each row of rangesA, I'm looking to find which (if any) row in rangesB fully contains the rangesA row - by which I mean rangesAChrom == rangesBChrom, rangesAStart >= rangesBStart and rangesAStop <= rangesBStop . Right now I'm doing the following, which I just don't like very much. Note that I'm looping over the rows of rangesA for other reasons, but none of those reasons are likely to be a big deal, it just ends up making things more readable given this particular solution. rangesA:

I have no idea what could be the problem here: I have some modules from Biopython which I can import easily when using the interactive prompt or executing python scripts via the command-line. The problem is, when I try and import the same biopython modules in a web-executable cgi script, I get a "Import Error" : No module named Bio Any ideas here? Here are a couple of possibilities: Apache (on Unix) generally runs as a different user, and with a different environment, to python from the command line. Try making a small script that just prints out sys.version and sys.prefix , and compare the