mkkir

#!/usr/local/bin/perl
##############################################################################
# SCRIPT NAME:	mkkir
# DESCRIPTION:	make the kir epitope files
# PARAMETERS:	none
# OUTPUT:	
# TABLES:       
#
# DATE WRITTEN: 2012-07-24
# WRITTEN BY:   Martin J. Maiers
#
# REVISION HISTORY: 
# REVISION DATE		REVISED BY	DESCRIPTION 
# ------- ----------	--------------	-------------------------------------
#
#       COPYRIGHT (C) 2011 NATIONAL MARROW DONOR PROGRAM.  
#               ALL RIGHTS RESERVED        
##############################################################################
use strict;    # always
use warnings;  # or else


my $asap = "HLA-A.sap";
my $bsap = "HLA-B.sap";
my $csap = "HLA-C.sap";

my $aw = "Aw.txt";
my $bw = "Bw.txt";
my $cw = "Cw.txt";



#
# C
#
open CSAP, $csap or die "$!: $csap";
open CW, ">$cw" or die "$!: $cw";

while(<CSAP>) {
  chomp;
  my ($loc, $allele, $sapstring) = split /	/;
  my $locallele = join '*', $loc, $allele;
  my ($saps, $epitope) = getEpitope($locallele, $sapstring);
  print CW join ('	', $locallele, $saps, $epitope), "\n";
}

#
# B
#
open BSAP, $bsap or die "$!: $bsap";
open BW, ">$bw" or die "$!: $bw";

while(<BSAP>) {
  chomp;
  my ($loc, $allele, $sapstring) = split /	/;
  my $locallele = join '*', $loc, $allele;
  my ($saps, $epitope) = getEpitope($locallele, $sapstring);
  print BW join ('	', $locallele, $saps, $epitope), "\n";
}

#
# A
#
open ASAP, $asap or die "$!: $asap";
open AW, ">$aw" or die "$!: $aw";

while(<ASAP>) {
  chomp;
  my ($loc, $allele, $sapstring) = split /	/;
  my $locallele = join '*', $loc, $allele;
  my ($saps, $epitope) = getEpitope($locallele, $sapstring);
  print AW join ('	', $locallele, $saps, $epitope), "\n";
}

exit 0;

sub getEpitope {
  my ($locallele, $sapstring) = @_;
  my ($loc, $allele) = split /\*/, $locallele;

  # Abi-Rached/Parham (2012) PLoS Genetics doi:10.1371/journal.pgen.1001192
  # "Lineage III KIR recognize the C1 and C2 epitopes of MHC
  # class I. C2 depends upon valine 76 (V76) and lysine 80 (K80), a
  # motif restricted to a subset of MHC-C allotypes. C1 depends upon
  # V76 and asparagine 80 (N80), a motif present in subsets of MHCC
  # and -B allotypes"

  # Parham (2013) Nature Reviews Immunology  Bw4 has Argenine 83
  # Lineage II KIRs recognize the HLA-A epitope A3/11 and the Bw4 epitope
  # of HLA-A and HLA-B

  # parse
  my %S;
  foreach (split / /, $sapstring) {
    /(\D)(\d+)/;
    my $aa = $1;
    my $pos = $2;
    $S{$pos} = $aa;
  }

  my $epitope = "X";

  if ($loc eq "HLA-C") {

    $epitope = "C1" if $S{80} eq "N" && $S{76} eq "V";

    $epitope = "C2" if $S{80} eq "K" && $S{76} eq "V" ;

    my $saps = join ' ', $S{77}."77", $S{80}."80";
    return ($saps, $epitope);
  } elsif ($loc eq "HLA-B") {
    # Parham (2013) Nature Reviews Immunology  Bw4 has Argenine 83
    $epitope = "Bw4" if $S{83} eq "R";

    # Parham (2013) Nature Reviews Immunology  Bw6 is not a KIR epitope
    #$epitope = "Bw6" if $S{83} eq "G";
 
    # some HLA-B have a C1 epitope
    # http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2973822/
    $epitope = "C1" if $S{80} eq "N" && $S{76} eq "V";

    my $saps = join ' ', $S{76}."76", $S{77}."77", $S{80}."80", $S{81}."81",$S{82}."82",$S{83}."83";
    return ($saps, $epitope);
  } elsif ($loc eq "HLA-A") {

    $epitope = "A311" if $allele=~/^03:/;
    $epitope = "A311" if $allele=~/^11:/;
    $epitope = "Bw4" if $S{83} eq "R";
    my $saps = join ' ', $S{76}."76", $S{77}."77", $S{80}."80", $S{81}."81",$S{82}."82",$S{83}."83";
    return ($saps, $epitope);
  } else {
    warn "invalid locus: $loc";
  }
  



}