README

RNAStructProfiling

To download source code, click on "zip" link on the RNAStructProfiling github
page (https://github.com/gtfold/RNAStructProfiling/zipball/master).

To compile on a Unix/Linus machine, make sure the following files are in the
same directory:
--main.c
--profile.h
--profile.c
--summaryGraph.c
--summaryGraph.h
--hashtbl.c
--hashtbl.h
--Makefile
--graph.c
--graph.h
--memoryDFS.c
--memoryDFS.h

Open a terminal window, navigate to the directory that contains
the above files, and type 'make' to compile the program.

To run, you will need to input 1) a sequence file, and 2) an
sfold 'sample_1000.out' file, or any other structure file that
lists structures in triplet notation, with the delineation
"Structure [number]" on a separate line before every structure.
(Included in the github repository is a sequence file and a sample
file from ecoli5S that may be used to run the program.)

Usage (from within that same directory): 
./RNAprofile [seq file] [sample file] [options]

Common options:
-h [percent] = filter out all helix classes that occur in less than [h] percent
 of the input sample structures
-p [percent] = filter out all profiles that occur less than [p] percent of the
 input sample structures
-g = disable graph making component of program (if only interested in helix and
 profile stats)
-o [file name] = produces the output graphviz dot file called [file name];
 'profile.dot' used by default