deltaSVM README file
====================

  deltasvm.pl is a simple perl script that calculates the changes in SVM
  weights.  Please cite the following paper if you use our method:

  Lee D*, Gorkin DU*, Baker M, Strober BJ, Asoni AL, McCallion AS, and Beer MA.
  Predicting the Impact of Regulatory Variants From DNA Sequence. Submitted.
  * Co-first

Tutorial
========

  deltasvm.pl takes 4 input parameters as follows:
    ref_seq_file
    alt_seq_file
    svm_weight_file
    output_file

  As an example, we provide sample files along with the script.  ref_seq_ex.fa
  has three 19bp sequences centered at the three SNPs (rs11102967, rs1277917,
  and rs12740374) with reference alleles.  Similarly, alt_seq_ex.fa also has
  the three sequences.  Please note that they should be in the exactly same
  order with the same sequence id.  Also, all sequences should be written in one
  line (new lines are not allowed within a sequence).

  Now you can calculate the deltaSVM scores for these SNPs using any SVM weight
  file.  As a simple exercise, download the SVM weight file trained on HepG2 DHS
  from the following URL:

  http://www.beerlab.org/deltasvm/downloads/SupplementaryTable_hepg2weights.txt

  And type:
  $ perl deltasvm.pl ref_seq_ex.fa alt_seq_ex.fa SupplementaryTable_hepg2weights.txt test_output.txt

  test_output.txt will look like the following (also included as output_ex.txt):

  rs11102967      0.130464
  rs1277917       1.652959
  rs12740374      7.359249

  If you have any question, please send me an email at dwlee AT jhu DOT edu
