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Kevin
2026-04-29 23:01:54 +02:00
parent d0b12d668d
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nextflow/tests-v1/bin/AMPA.pl Executable file
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#!/usr/bin/perl -w
use strict;
use Math::CDF;
use Math::Round;
#
# The default input parameters
#
my $debug = 0;
my $noplot = 0;
my $gnuplot = "";
my $input_file = "protein.txt";
my $window_size = 7;
my $threshold = 0.225;
my $graph_file = "";
my $result_file = "results.$$";
my $data_file = "sliding.$$";
my $_prompt = "";
#
# Find out gnuplot
#
if( exists $ENV{GNUPLOT_BIN}) {
$gnuplot = $ENV{GNUPLOT_BIN};
}
if( $gnuplot eq "" ) {
$gnuplot = `which gnuplot`;
chomp($gnuplot);
}
if( $gnuplot eq "" ) {
print "AMPA requires gnuplot to be installed on your system.";
exit 2;
}
#
# Parse the command
#
my $cl=join( " ", @ARGV);
if (($cl=~/-h/) ||($cl=~/-H/) ) {
# print usage
print "Usage: AMPA.pl -in=<input fasta file> [other options]\n";
print "\n";
print "Available options:\n";
print "-in Fasta sequence input file\n";
print "-t Threshold value (default: 7)\n";
print "-w Window size value (default: 0.225)\n";
print "-rf File where store the program result\n";
print "-df File where store the produced plot data\n";
print "-gf File where store the generated plot\n";
print "-noplot Skip plot creation step\n";
exit 1;
}
#
# If not command line is provided switch to interactive mode
#
if ($#ARGV==-1 ) {
# the input file name
print "Enter the name of the sequence file and then press Enter [$input_file]: ";
$_prompt = <STDIN>;
chomp($_prompt);
if( $_prompt ne "" ) { $input_file=$_prompt };
# the window size
print "Enter the desired window size as an odd number and then press Enter [$window_size]: ";
$_prompt = <STDIN>;
chomp($_prompt);
if( $_prompt ne "" ) { $window_size = $_prompt };
# the threshold
print "Enter the desired threshold and then press Enter [$threshold]: ";
$_prompt = <STDIN>;
chomp($_prompt);
if( $_prompt ne "" ) { $threshold = $_prompt };
}
# option '-in': input file name
if ( ($cl=~/-in=\s*(\S+)/)) {
$input_file = $1;
}
# option '-w': window size
if ( ($cl =~ /-w=\s*(\S+)/)) {
$window_size = $1;
}
# option '-t': threshold value
if ( ($cl =~ /-t=\s*(\S+)/)) {
$threshold = $1;
}
# option '-gf': output graph file
if ( ($cl =~ /-gf=\s*(\S+)/)) {
$graph_file = $1;
}
# option '-rf': output result file
if ( ($cl =~ /-rf=\s*(\S+)/)) {
$result_file = $1;
}
# option '-df': output sliding file
if ( ($cl =~ /-df=\s*(\S+)/)) {
$data_file = $1;
}
# option '-debug': enable debug mode
if ( ($cl =~ /-debug/)) {
$debug = 1;
}
# option '-noplot': threshold value
if ( ($cl =~ /-noplot/)) {
$noplot = 1;
}
if( $debug != 0 ) {
print "Window size : $window_size\n";
print "Threshold value : $threshold\n";
print "Input file name : $input_file\n";
print "Graph file name : $graph_file\n";
print "Result file name : $result_file\n";
print "Data file name : $data_file\n";
print "Gnuplot bin : $gnuplot\n";
}
#
# Main script start here
#
my(@names,@lengths,@sequences,$sequence_number,$protein);
open(PROTEIN, "$input_file") or die "Cannot open '$input_file': $!\n";
#The program should read the user input sequence
$/ = ">";
for(my $c=1; $c<(($window_size + 1)/2); $c++) {
push (@sequences, 'X');
}
while (my $sequence_record = <PROTEIN>) {
if ($sequence_record eq ">") {
next;
}
my $sequence_name = "";
if ($sequence_record =~ m/([^\n]+)/) {
$sequence_name = $1;
} else {
$sequence_name = "No title was found!";
}
$sequence_record =~ s/[^\n]+//;
push (@names, $sequence_name);
$sequence_record =~ s/[^ACDEFGHIKLMNPQRSTVWYacdefghiklmnpqrstvwy]//g;
push (@sequences, $sequence_record);
push (@lengths, length($sequence_record));
my $sequence_length = length($sequence_record);
}
for(my $c=1; $c<(($window_size + 1)/2); $c++) {
push (@sequences, 'X');
}
my $sequences = join("",@sequences);
close(PROTEIN) or die "Cannot close the file: $!\n";
#The program calls the subroutines to analyze the sequence
&sliding($sequences);
if(!$noplot) {
&gnuplot_sld();
}
### Subroutines
# Defines the value at the window center (window_size+1)/2
sub sliding {
open(KD,">$data_file") or die("Could not open '$data_file': $!\n");
open(RS,">$result_file") or die("Could not open '$result_file': $!\n");
my($center,$length);
my $half = (($window_size + 1)/2);
# These are the antimicrobial propensity values for each amino acid
my %sliding = (
'A', 0.307,
'R', 0.106,
'N', 0.240,
'D', 0.479,
'C', 0.165,
'Q', 0.248,
'E', 0.449,
'G', 0.265,
'H', 0.202,
'I', 0.198,
'L', 0.246,
'K', 0.111,
'M', 0.265,
'F', 0.246,
'P', 0.327,
'S', 0.281,
'T', 0.242,
'W', 0.172,
'Y', 0.185,
'V', 0.200,
'X', $threshold
);
$protein = shift;
print KD "# The window size is currently set at $window_size.\n";
print KD "# Here are the AMSI values for this protein:\n";
print KD "# $names[0]\n";
print KD "# Pos\ APV\n";
print KD "# ---\t-------------------\n";
my $acc1=0;
my $acc2=0;
my $bacindex=0;
my $amvalue=0;
my $bacvalue=0;
my $prob=0;
for(my $i=0;$i<=(length($protein)-$window_size);$i++) {
my $window = substr($protein, $i, $window_size);
my $sum=0;
for(my $j=0; $j<$window_size; $j++) {
my $PV = 0;
my $residue = substr($window, $j, 1);
$PV = $sliding{$residue};
$sum+=$PV;
}
$center = $i + $half;
my $position = $center - 3;
my $APV=$sum/$window_size;
$APV = sprintf "%.3f", $APV;
print KD "$position\t$APV\n";
$amvalue=$amvalue+$APV;
if($acc1==3) {
if($acc2>=10){
my $init=$position-$acc2-2;
my $last=$position-1;
my $bacvalue=(($bacvalue)/($last-$init+1));
$prob = &Math::CDF::pnorm(($bacvalue-0.2584)/0.02479);
$prob*=100;
my $rbacvalue = nearest(.001, $bacvalue);
my $rprob = nearest(1, $prob);
print RS "Antimicrobial stretch found in $init to $last. Propensity value $rbacvalue ($rprob %) \n";
$bacindex++;
$acc2=0;
$acc1=0;
$bacvalue=0;
$prob=0;
}
if($acc2<10){
$acc1=0;
$acc2=0;
$bacvalue=0;
}
}
if($acc1!=3){
if($acc2==0) {
$acc1=0;
$bacvalue=0;
}
if($APV<=$threshold) {
$acc2++;
$bacvalue+=$APV
}
if($APV>$threshold){
$acc1++;
$bacvalue+=$APV
}
}
if($position==(length($protein)-(($window_size)-1)) && $acc2>=10) {
my $init=$position-$acc2-2;
my $last=$position-1;
my $bacvalue=(($bacvalue)/($last-$init+1));
$bacindex++;
$prob = &Math::CDF::pnorm(($bacvalue-0.2584)/0.02479);
$prob*=100;
my $rbacvalue = nearest(.001, $bacvalue);
my $rprob = nearest(1, $prob);
print RS "Antimicrobial stretch found in $init to $last. Propensity value $rbacvalue ($rprob %) \n";
}
}
print RS "# This protein has $bacindex bactericidal stretches \n";
my $manvalue = nearest(.001, $amvalue/(length($protein)-6));
print RS "# This protein has a mean antimicrobial value of $manvalue \n";
close(KD) or die("Could not close file: $!\n");
}
sub gnuplot_sld {
my $cmdline = "|$gnuplot -persist";
open (GP, $cmdline) or die "no gnuplot";
# force buffer to flush after each write
use FileHandle;
GP->autoflush(1);
print GP "set title \"Antimicrobial Profile\"\n";
print GP "set xlabel \"Position\"\n";
print GP "set ylabel \"Score\"\n";
print GP "set grid\n";
print GP "set data style lines\n";
# if an output has been specified output to it
if( $graph_file ne "" ) {
print GP "set terminal png large enhanced size 800 600\n";
print GP "set output '$graph_file' \n";
}
print GP "plot \"$data_file\" u 1:2 t \"Antimicrobial profile \" w lines\n";
close GP;
}