NMR Peak Assigner Perl

#!/usr/bin/perl
#
#  For NMR Peak Assignment using known assignments
#  tries to match picked peaks to assignments based on
#  peak closest distance
#
#
# ./nmrasser.pl <picked peaks> <peak assignments>
#
#
#
# picked peaks file should be from NMRviewJ
# Assigned peaks file should be of the format
# Kind of Ugly but it works
# Residue #. HN/N Chemicalshift
#
# ex.
# 1. HN 9.3
# 1. N  120.2

use Math::Complex;

my %hn = ();
my %n = ();
my %npeaks = ();
my %hnpeaks  = ();
$x = 0;

if(!$ARGV[0]){  die "Need your picked peaks to parse!"; }
if(!$ARGV[1]) { die "Need your peak assignments!"; }

open(PEAKS, $ARGV[0]);
open(ASS, $ARGV[1]);
open(OUTPUT, "$ARGV[0].out");

if($ARGV[2])
  {open(SEQ, $ARGV[2]);
   @seq = <SEQ>;
   }

@peaks = <PEAKS>;
@ass = <ASS>;



#find 1Hppm and N15 ppm for each peak
foreach $line (@peaks)
{

   if($line =~ m/\{\}/)
   {
    @ln = split(/ /, $line);
     $hnpeaks{ $ln[0] } = $ln[2];
     $npeaks{ $ln[0] } = $ln[9];
     #print "$ln[2] : $ln[9] \n";
   }
   #  else { print "BALLS\n!"; }
}

#Finds location of 1H N15 peaks from assignments

$a=1;
foreach $line1 (@ass)
{

   if($line1 =~ m/\d{1,3}\.N /)
   {
      @nit = split(/\s{1,6}/, $line1);
       #print "$nit[0] $nit[1]\n";
      @stuff = split(/\./, $nit[0]);
       #Assign H peak to a number
       $n{ $stuff[0] } = $nit[1];
       #$n{ $stuff[0] }->{ seq } = substr($seq[0],$a,1);
       $a++;
   }

   if($line1 =~ m/\d{1,3}\.HN /)
   {   @hnit = split(/\s{1,7}/, $line1);
       #print "$hnit[0] $hnit[1]\n";
       @stuff1 = split(/\./, $hnit[0]);
       $hn{ $stuff1[0] } = $hnit[1];
   }


     #else { print "CRAP!\n"; }


}

#print "assigns: $a\n\n";
#foreach $key (keys %n) {
#print "$key $n{ $key } $hn{ $key }\n";
#}



foreach $keay (sort keys %npeaks)
{

  &matcher($keay,0);


}

foreach $keyr (keys %npeaks) {
  &removedups($keyr,1);

}

foreach $keyr (keys %npeaks) {
  &removedups($keyr,2);

}

foreach $keyr (keys %npeaks) {
  &removedups($keyr,3);

}

foreach $keyr (keys %npeaks) {

  &removedups1($keyr);

}







$x=0;
foreach $key (sort keys %npeaks) {

if($npeaks->{$key}->{ winname }->{0} > 0) { $x++; }
 printf("%d N:%f HN:%f : %d N:%f HN:%f ::: %f \n",$key,  $npeaks{$key}, $hnpeaks{$key}, $npeaks->{$key}->{ winname }->{0}, $n{$npeaks->{$key}->{ winname }->{0} }, $hn{$npeaks->{$key}->{ winname }->{0}}, $npeaks-> {$key}->{ winner }->{0});

}


print "Number matches: $x\n";


close(OUTPUT);
close(PEAKS);
close(ASS);
#close(SEQ);

exit;

sub matcher
{

# print "###### $_[0]\n\n\n\n\n\n\n\n";

$num = $_[0];



 $npeaks->{ $num }->{ winner }->{0} = 1;

 foreach $keym (sort keys %hn )
 {
    #print "$npeaks{ $num } ** $n{ $keym } ** $hnpeaks{ $num }  ** $hn{ $keym}\n";


    $rise = abs($npeaks{ $num } - $n{ $keym });
    $run = abs($hnpeaks{ $num } - $hn{ $keym});
    $c = sqrt($rise**2 + $run**2);
    #print "$rise **** $run ***** $c\n\n\n";

    if($npeaks->{ $num }->{ winner }->{0} > $c && $c < 0.25)
     {

        $npeaks->{ $num }->{ winner }->{1} = $npeaks->{ $num }->{ winner }->{0}; $npeaks->{ $num }->{ winname }->{1} = $npeaks->{ $num }->{ winname }->{0};
        $npeaks->{ $num }->{ winner }->{2} = $npeaks->{ $num }->{ winner }->{1}; $npeaks->{ $num }->{ winname }->{2} = $npeaks->{ $num }->{ winname }->{1};
        $npeaks->{ $num }->{ winner }->{3} = $npeaks->{ $num }->{ winner }->{2}; $npeaks->{ $num }->{ winname }->{3} = $npeaks->{ $num }->{ winname }->{2};
        $npeaks->{ $num }->{ winner }->{0} = $c; $npeaks->{ $num }->{ winname }->{0} = $keym;
}

    #print "$n{$keym} : $hn{$keym}\n";




 }



#print "$npeaks->{ $num }->{ winname }->{3}\n\n\n";


}#sub

sub removedups
{


my($keyp,$nt)=@_;

foreach $key1 (keys %npeaks) {

if($keyp != $key1 && $npeaks->{ $keyp }->{ winname }->{0} == $npeaks->{ $key1 }->{ winname }->{0})
  {
   if($npeaks->{ $keyp }->{ winner }->{0} > $npeaks->{ $key1 }->{ winner }->{0})
   {

      $npeaks->{ $keyp }->{ winner }->{0} = $npeaks->{ $keyp }->{ winner }->{$nt};
      $npeaks->{ $keyp }->{ winname }->{0} = $npeaks->{ $keyp }->{ winname }->{$nt};



   }

      else {
           $npeaks->{ $key1 }->{ winner }->{0} = $npeaks->{ $key1 }->{ winner }->{$nt};
           $npeaks->{ $key1 }->{ winname }->{0} = $npeaks->{ $key1 }->{ winname }->{$nt};

            #if(removedups1($key1,$nt+1) == -1){ print "POOP\n\n"; return 0;}
           }

  }
}#foreach


}#sub



sub removedups1
{

my($keyp) = $_[0];


my($key1);

foreach $key1 (keys %npeaks) {


if($keyp != $key1 && $npeaks->{ $keyp }->{ winname }->{0} == $npeaks->{ $key1 }->{ winname }->{0})
  {
   if($npeaks->{ $keyp }->{ winner }->{0} > $npeaks->{ $key1 }->{ winner }->{0})
   {

      $npeaks->{ $keyp }->{ winner }->{0} = 0;
      $npeaks->{ $keyp }->{ winname }->{0} = 0;



   }

      else {
           $npeaks->{ $key1 }->{ winner }->{0} = 0;
           $npeaks->{ $key1 }->{ winname }->{0} = 0;

           }
  }
}#foreach


}#sub