join

Usage::

join.py [options] filea:col# fileb:col#

join filea with fileb by looking for the same value in col#

col numbers are 0-based indexing.

can never get linux join to work as i want. also handles files with different seperators.

Options:

-h, --help	show this help message and exit
--sepa=SEPA	separator for 1st file
--sepb=SEPB	separator for 2nd file
-x	only print the shared column once.

gene-list overlap

Uses the hypergeometric distribtion to calculate the probality of gene-list overlap. Given 2 lists (or gene sets) we know they came from, e.g. GG genes and we know there are AA genes in list-A and BB genes in list-B. What is the probability that they share SS genes?

$ ./list_overlap_p.py SS GG AA BB

e.g.:

$ ./list_overlap_p.py 10 30000 345 322
0.0043679470685

gives the probability that 10 genes are shared in 2 random lists of length 345 and 322 given that those lists are drawn from a set of 30K genes.