README

DomPred & DomSSEA are the work of Liam McGuffin and Russel Marsden

This repo contains the DomSSEA components for parsing a psipred .horiz files and outputting
dompred domain boundary predictions. With the components for make a Dompred prediction as per
R.Marsden's work (parseDS.pl)

Note that you need the data files available via:
http://bioinfadmin.cs.ucl.ac.uk/downloads/dompred_data/
Download the tarball and place the contents in the data/ directory

Instalation
^^^^^^^^^^^

1) tar -zxvf dompred_data.tar.gz

	 Ensure everything ends up in a data/ directory inside the dompred directory
	 this will contain all the underlying datafiles including an ancient version
	 of pfamA. To my knowledge this pfamA file is not longer available at pfamA
	 but dompred critically depends on this specific file and if you change it
	 the predictions are worse.

2) compile DomSSEA
	cd src
	javac DomSSEA.java

Running a DomPRED job
^^^^^^^^^^^^^^^^^^^^^
1) Run a psipred job and find the .horiz file
2) Run blast vs the PfamA in the data tarball to produce a blast output
   called .blastdom
   blastpgp -i  input_seq -j 5 -a 2 -m 0 -b 1000 -d pfamA  > example.blastdom"
3) Run DomSSEA
	java DomSSEA [path and prefix to .horiz] [All_cut3 path]
	example where you have example.horiz:
		java DomSSEA example /dompred/data/All_cut3
4) Run parseDS.pl
  Something like:
	parseDS.pl example.domssea seqyes PfamA 0.01 5 domsseayes ppyes secproyes in /opt/Code/dompred/data/uniref90_PfamA /tmp/in /opt/Code/dompred/data/ /bin/gnuplot

TODO:
parseDS_fixattempt.pl : resolve the hundreds of runtime errors one day...