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psm_aller.pl
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#!/usr/bin/perl
######## FuzzyAPP #####################
# Developed by SARAVANAN VIJAYAKUMAR
# Centre for Bioinformatics, Pondicherry University
# Date: 14-2-2013
#
######Required Modules
my $PATH_EXE = "/home/user/Documents/Softwares/FuzzyApp-master/";
use List::Util qw[max];
my $PATHJAR = $PATH_EXE.'weka.jar';
##############Sequence Input via arguments
$Sequence_In = @ARGV[0];
#~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~BINOM FEATURE Calc
$Arff = "\@relation whatever\n\n\@attribute 1 numeric\n\@attribute 2 numeric\n\@attribute 3 numeric\n\@attribute 4 numeric\n\@attribute 5 numeric\n\@attribute 6 numeric\n\@attribute 7 numeric\n\@attribute 8 numeric\n\@attribute 9 numeric\n\@attribute 10 numeric\n\@attribute 11 numeric\n\@attribute 12 numeric\n\@attribute 13 numeric\n\@attribute 14 numeric\n\@attribute 15 numeric\n\@attribute 16 numeric\n\@attribute 17 numeric\n\@attribute 18 numeric\n\@attribute 19 numeric\n\@attribute 20 numeric\n\@attribute 21 numeric\n\@attribute 22 numeric\n\@attribute 23 numeric\n\@attribute 24 numeric\n\@attribute 25 numeric\n\@attribute 26 numeric\n\@attribute 27 numeric\n\@attribute 28 numeric\n\@attribute 29 numeric\n\@attribute 30 numeric\n\@attribute 31 numeric\n\@attribute 32 numeric\n\@attribute 33 numeric\n\@attribute 34 numeric\n\@attribute 35 numeric\n\@attribute 36 numeric\n\@attribute 37 numeric\n\@attribute 38 numeric\n\@attribute 39 numeric\n\@attribute 40 numeric\n\@attribute 41 numeric\n\@attribute 42 numeric\n\@attribute 43 numeric\n\@attribute 44 numeric\n\@attribute 45 numeric\n\@attribute 46 numeric\n\@attribute 47 numeric\n\@attribute 48 numeric\n\@attribute 49 numeric\n\@attribute 50 numeric\n\@attribute 51 numeric\n\@attribute 52 numeric\n\@attribute 53 numeric\n\@attribute 54 numeric\n\@attribute 55 numeric\n\@attribute 56 numeric\n\@attribute 57 numeric\n\@attribute 58 numeric\n\@attribute 59 numeric\n\@attribute 60 numeric\n\@attribute LABEL { A , N } \n\n\n\@data\n";
$Arff.= &Type_I($Sequence_In).",".&Type_II($Sequence_In).",".&Type_III($Sequence_In).","."A\n";
####Storing arff
my $path_info = '';
my $File_string=$path_info.&generate_random_string(8);
$File_string.='.arff';
open(TTT,">$File_string");
print TTT $Arff;
close(TTT);
$Arff="";
#####Adaboost Prediction
my $Machine_res = &ML_Test("$PATH_EXE/AN.model",$File_string);
print $Machine_res;
unlink($File_string);
#######End!
#################################### Vector Calc
sub Type_I{
my($param_one)=@_;
$param_one = uc $param_one;
@SLC = qw(A C D E F G H I K L M N P Q R S T V W Y);
$Length_Prt = length($param_one);
my $i=0;
# Measure Calculation
foreach(@SLC){
if($param_one =~m/$SLC[$i]/g){
$nX[$i] = ($param_one =~s/$SLC[$i]/$SLC[$i]/g);
}else{
$nX[$i] = 0;
}
$i++;
}
#Measure Calculation
for($i=0;$i<$Length_Prt;$i++){
$pX[$i] = $nX[$i]/$Length_Prt;
#$pX[$i] = sprintf "%.2f",$pX[$i];
}
#Theoretical Mean Calculation
@Res_Codon_Occ = qw(4 2 2 2 2 4 2 3 2 6 1 2 4 2 6 6 4 4 1 2);
my $j=0;
foreach(@Res_Codon_Occ){
$piX[$j] = $Res_Codon_Occ[$j]/61;
#$piX[$j] = sprintf "%.2f",$piX[$j];
$j++;
}
#Theoretical variance Calculation
for($i=0;$i<20;$i++){
$Theo_Variance[$i] = ($piX[$i]*(1-$piX[$i]))/$Length_Prt;
#$Theo_Variance[$i] = sprintf "%.2f",$Theo_Variance[$i];
}
#Type I Parameter Calculation
for($i=0;$i<20;$i++){
eval{($pX[$i] - $piX[$i])/(sqrt($Theo_Variance[$i]));};
if($@){
$Type_I_Value[$i] = 0.00;
}else{
$Type_I_Value[$i] = ($pX[$i] - $piX[$i])/(sqrt($Theo_Variance[$i]));
#$Type_I_Value[$i] = sprintf "%.2f", $Type_I_Value[$i];
}
}
$vector1 = join(",",@Type_I_Value);
return $vector1;
}
############################################################################
sub TRACE_POS{
my($STRING,$CHAR)= @_;
my $ixyz=0;
my $sum=0;
do{
$Holder[$ixyz] = index($STRING,$CHAR,$Crawler)+1;
$sum+=$Holder[$ixyz];
$Crawler = $Holder[$ixyz];
$ixyz++;
$ex = index($STRING,$CHAR,$Crawler);
}until ($ex == -1);
return $sum;
}
###########################################################################
sub Type_II{
my($param_two) = @_;
$param_two = uc $param_two;
@SLC = qw(A C D E F G H I K L M N P Q R S T V W Y);
$Length_Prt = length($param_two);
my $i=0;
#Measure Calculation
foreach(@SLC){
if($param_two =~m/$SLC[$i]/g){
$nX[$i] = ($param_two =~s/$SLC[$i]/$SLC[$i]/g);
}else{
$nX[$i] = 0;
}
$i++;
}
for($i=0;$i<20;$i++){
if($nX[$i] == 0){
$M_m[$i] = 0.0;
$T_v[$i]= 0.0;
$P_V[$i] = 0.0;
}else{
$M_m[$i]= &TRACE_POS($param_two,$SLC[$i])/$nX[$i];
$T_v[$i] = (($Length_Prt+1)*($Length_Prt-$nX[$i])/(12*$nX[$i])); #Theoritical Variance Calculation
$T_m[$i] = ($Length_Prt+1)/2; #Theoritical Mean
$P_V[$i] = ($M_m[$i]-$T_m[$i])/(sqrt($T_v[$i])); #Parameter Value Calculation
}
}
$vector2 = join(",",@P_V);
@SLC=();
@nX=();
@M_m=();
@T_v=();
@P_V=();
return $vector2;
}
###################################
sub COMPLEX_POS{
my($STRING,$CHAR)= @_;
my $i=0;
my $sum=0;
my $Crawler=0;
my $ex;
my $k;
do{
$HolderX[$i] = index($STRING,$CHAR,$Crawler)+1;
$sum+=$HolderX[$i];
$Crawler = $HolderX[$i];
$i++;
$ex = index($STRING,$CHAR,$Crawler);
}until ($ex == -1);
$ret=0;
for($k=0;$k<@HolderX;$k++){
$elite = ($STRING=~s/$CHAR/$CHAR/g);
if($elite!= 0){
$ret+= ($HolderX[$k]- (($sum/$elite)))**2;
}else{
$ret+=0;
}
}
@HolderX=();
return $ret;
}
###################################
sub Type_III{
my($param_three) = @_;
@SLC = qw(A C D E F G H I K L M N P Q R S T V W Y);
$Length_Prt = length($param_three);
my $i=0;
foreach(@SLC){
if($param_three =~m/$SLC[$i]/g){
$nX[$i] = ($param_three =~s/$SLC[$i]/$SLC[$i]/g);
}else{
$nX[$i] = 0;
}
$i++;
}
$const1 = ($Length_Prt-1)/$Length_Prt;
for($i=0;$i<20;$i++){
if($nX[$i] == 1){
$const2 = 0.0;
}else{
$const2 = 1/($nX[$i]-1);
}
$const3 = &COMPLEX_POS($param_three,$SLC[$i]);
$Me_m[$i] = $const1*$const2*$const3;#Measure 3
$Te_m[$i] = (($Length_Prt**2)-1)/12;
if($nX[$i]==0){
$Te_v[$i] = 0;
}else{
if($nX[$i] == 1){
$Te_v[$i] = 0.0;
}else{
$Te_v[$i] = (($Length_Prt-$nX[$i])*(($Length_Prt-1)**2)*($Length_Prt+1)*((2*$nX[$i]*$Length_Prt)+(3*$Length_Prt)+(3*$nX[$i])+3))/(360*$nX[$i]*($nX[$i]-1)*$Length_Prt);
}
}
if($Te_v[$i]!=0){
$F_V[$i] = ($Me_m[$i]-$Te_m[$i])/(sqrt($Te_v[$i])); #Parameter Value Calculation
}else{
$F_V[$i]= 0.0;
}
# print $F_V[$i]."\n";
}
$vector3 = join(',',@F_V);
@SLC=();
@nX=();
@Te_v=();
@F_V=();
return $vector3;
}
sub ML_Test{
my($MODEL,$fil,$xsav)= @_;
#my $result = `java -classpath weka.jar weka.classifiers.meta.AdaBoostM1 -T $fil -l $MODEL -p 0`;
my $result = `java -classpath $PATHJAR weka.classifiers.meta.AdaBoostM1 -T $fil -l $MODEL -p 0`;
#$result=~s/ //g;
#my @Cont = split('\n',$result);
return $result;
}
###########
sub generate_random_string
{
my $length_of_randomstring=shift;# the length of
# the random string to generate
my @chars=('a'..'z','A'..'Z','0'..'9');
my $random_string;
foreach (1..$length_of_randomstring)
{
# rand @chars will generate a random
# number between 0 and scalar @chars
$random_string.=$chars[rand @chars];
}
return $random_string;
}