Instructions

How to use this code (With apologies if there's an insulting level of detail):

1) You'll need the development version of Easel.  Go to github.com/EddyRivasLab and clone the easel repo.  CD into the easel directory and do "git checkout -b development remotes/origin/develop"

2) Build easel with:
a) autoconf
b) ./configure
c) make dev <- you need to make the dev variant to build the program that creates dsq format sequence databases

3) Build the code in this directory.
a) Edit the makefile to specify the path to the version of easel you just built.
b) make

That will create the skeleton count_occurrences program

4) You need to create versions of your sequence databases in HMMER4 format with the esl_dsqdata_example2 program in your easel directory.  The syntax is esl_dsqdata_example2 <input file in fasta format> <output filename>.  That will create about five files with different suffixes after <output filename>.

To run the count_occurences program do: count_occurrences <number> <output filename>.  Right now it just counts statistics about the input database, but you'll change that.