README

Welcome to radar

radar is free software. Please see the file COPYING for details. 

1. Requirements

RADAR is written in ANSI C and should compile on most platforms. The
executable is called 'radar'. There is a python installation, which 
requires cython (http://cython.org) for compilation and will install
'radar.py'

Both radar and radar.py require the lfasta program from W.R. 
Pearson's fasta package. To install this, execute the following
commands:

	mkdir fasta2
	cd fasta2
	wget http://faculty.virginia.edu/wrpearson/fasta/fasta2/fasta2.shar.Z
	gunzip fasta2.shar.Z
	sh fasta2.shar
	make lfasta

Copy the newly built 'lfasta' executable into a directory on your
path.

2. Installation:
      
2.1 retrieve the latest from http://sourceforge.net/projects/repeatradar
           
2.2 extract source files
      
	tar -xvzf radar-x.x.x.tgz
	cd radar-x.x.x.tgz
	  
2.3 configure the package

	./configure
      
2.4 radar.py: installation python interface to radar (recommended)
      
	python setup.py install
      
	This will install radar.py in your path. Please make sure
	you have the appropriate permissions.
      
2.5 radar: classic installation of C executable
      
	make; make install

3. Usage of radar.py

Please execute 

	radar.py -h 
or 

	radar.py --help

for usage instructions. Radar.py accepts FASTA formatted input and can process
multiple sequences and files.

The simplest use case is

	radar.py < ./example/finc.fasta 

4.  Usage of radar (classic C executable)

Before you find out yourself, the user interface to radar is pretty 
basic and not very comfortable and fault-tolerant, hence the newer radar.py.
Unless you want to supply a multiple alignment to radar use of radar.py
is much more comfortable.

The basic usage is the following:

 	radar -P c -Q c -R c [-S c] [-V n]

where the parameters are
	-P filename of the multiple alignment
    -Q filename of lfasta-output
    -R filename of the sequence
    -S filename of sequence lfasta-file[optional]
    -V level of verbosity. 0 is lowest, 4 is highest.

The multiple alignment file should contain the rows separated
by newlines.
      
The sequence file should just contain the sequence.
      
The lfasta-files contain the output of the lfasta program.

See the directory ./example for templates for these files. You
can run the example by typing

	./src/radar -P example/finc.ma -Q example/finc.lfasta1 -R example/finc.seq -S example/finc.lfasta2
      
after compilation.

If you do not have a multiple alignment, you can also run radar
in single sequence mode. Simply provide the sequence itself as the multiple
alignment by providing the sequence twice:

     ./src/radar -P example/finc.seq -Q example/finc.lfasta1 -R example/finc.seq -S example/finc.lfasta2