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@brsaran
brsaran committed Jun 24, 2015
1 parent 02a4b91 commit 32dfcd5
Showing 1 changed file with 25 additions and 21 deletions.
46 changes: 25 additions & 21 deletions source/LBEEP.pl
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#!/usr/bin/perl
###################################################################################
# Author: Saravanan Vijayakumar (brsaran@gmail.com) #
# Affiliation: CAS in Crystallography and Biophysics, University of Madras, India #
# Date: 18-05-2015 #
###################################################################################
use strict;
use Cwd qw(abs_path);
use lib abs_path().'/dependency/module/';
use brsaran::DDE;

use lib abs_path().'/dependency/module/'; #setting module dependnecy path ! Do not change unless you are sure !
use brsaran::DDE; #requires DDE module developed in this study

##########################

my $path2WEKA = abs_path().'/dependency/'; #change only if weka.jar is in some other location;

#########################

####### DO not change anyhting beyond this line ###############
####### DO not change anyhting beyond this line, unless if you are sure ###############

###Argument Check~~~~~~~~~~~~
my ($i, $mode, $inFile, $outFile,$Thresh,$MODEL);
Expand All @@ -35,7 +39,7 @@
if($ARGV[$i] eq "-M"){
$MODEL = $ARGV[$i+1];
$MODEL=~s/\s//g;
if(($MODEL ne 'B') && ($MODEL ne 'O')){ print "-M $MODEL invalid option! use 'B' or 'O' Exiting !\n"; exit;}
if(($MODEL ne 'B') && ($MODEL ne 'O')&&($MODEL ne 'C')){ print "-M $MODEL invalid option! use 'B' or 'O' or 'C' Exiting !\n"; exit;}
}
if($ARGV[$i] eq "-t"){
$Thresh = $ARGV[$i+1];
Expand All @@ -53,11 +57,12 @@


##################### PEPTIDE MODE BEGINS #####################################
my (@FHead,@PEP,@PRO,@Result,$Pep_DDE,$j,$line1,$line2,$temp,$Arff_header,$Pro_Out,$Pep_Out,$FinalOutPep);
$FinalOutPep = 'Sno,ID|Peptide|,Score'."\n";
$j=0;

if($mode eq "pep"){
my (@FHead,@PEP,@PRO,@Result,$Pep_DDE,$j,$line1,$line2,$temp,$Arff_header,$Pro_Out,$Pep_Out,$FinalOutPep); #Variable decclaration
$FinalOutPep = 'Sno,ID|Peptide|,Score'."\n"; #Header for CSV
$j=0; #Variable for counting the peptides

if($mode eq "pep"){ #If peptide mode is opted
$FinalOutPep = 'Sno,ID|Peptide|,Score'."\n";
print "\nProcessing Input...........";
while(($line1 = <INFILE>) && ($line2 = <INFILE>)){
Expand All @@ -83,8 +88,8 @@
$Pep_DDE=""; #Release memory
print "Prediction.................";
$Pep_Out = Epi_Predict_pep($temp,$path2WEKA,$MODEL); #Make prediction
$Pep_Out=~s/^(?:.*\n){1,5}//; #Remove line 1-5
$Pep_Out=~s/(?:.*\n){1,1}\z//; #Remove last line
$Pep_Out=~s/^(?:.*\n){1,5}//; #Remove line 1-5 of weka out
$Pep_Out=~s/(?:.*\n){1,1}\z//; #Remove last line of weka out
`rm $temp`; #remove ARFF file
print "Done\n";

Expand All @@ -108,11 +113,12 @@
###### PEPTIDE MODE ENDS ###########################

############################# Protein Mode Begins ##########################
$j=0;
my ($PFhead, $protein,@Position);
$j=0; #Reinitializing $j

my ($PFhead, $protein,@Position); #Variable Decclaration for protein mode

if($mode eq "pro"){
$FinalOutPep = 'Position,|Peptide|,Score'."\n";
if($mode eq "pro"){# If protein mode is opted
$FinalOutPep = 'Position,|Peptide|,Score'."\n"; #Header for CSV
print "\nEnter the Window size to be scanned (6-15):";
my $Window = <STDIN>;
chop($Window);
Expand All @@ -127,7 +133,7 @@
print "\nWindow size not between 6 and 15 ! May obtain undesired result !\n";
}
close (INFILE);
######## Split the protein into mentioned window size and ARFF #################
######## Split the protein into mentioned window size and generating inputs #################
print "\nSplitting the Sequence into the mentioned Window Size........";
my $Length_Protein = length($protein);
for($j=0;$j<($Length_Protein - ($Window-1));$j++){
Expand All @@ -146,7 +152,7 @@
$Pep_DDE = "";
print "Done\n";
print "Prediction............";
$Pro_Out = Epi_Predict_pep($temp,$path2WEKA,$MODEL); #Make prediction
$Pro_Out = Epi_Predict_pep($temp,$path2WEKA,$MODEL);#Make prediction
$Pro_Out=~s/^(?:.*\n){1,5}//; #Remove line 1-5
$Pro_Out=~s/(?:.*\n){1,1}\z//; #Remove last line
`rm $temp`; #remove ARFF file
Expand Down Expand Up @@ -177,7 +183,7 @@
chop($Ht);
while (uc $Ht eq 'Y'){
print "Generating HTML Output......................";
my $HTML_head = '<!DOCTYPE html><html><body><body bgcolor="#E6E6FA"><H1><center>L-BEEP V1.0</H1><br><H2> <center>Results for the Input Protein: <font color = "blue">'. substr($PFhead,1,10).'</font></H2><br><br>'."<H4><font color = 'red'>Parameters: -i: $inFile\; -m: $mode\; -M: $MODEL\; -t: $Thresh\; Window_size: $Window</font></h4>".'<hr><br><pre>';
my $HTML_head = '<!DOCTYPE html><html><body><body bgcolor="#E6E6FA"><H1><center>LBEEP V1.0</H1><p><H4><center><font color = "green">CAS in Crystallography and Biophysics,<br>University of Madras, Chennai - 600025. Tamilnadu, India.</center></font><br><H2> <center>Results for the Input Protein: <font color = "blue">'. substr($PFhead,1,10).'</font></H2><br><br>'."<H4><font color = 'red'>Parameters: -i: $inFile\; -m: $mode\; -M: $MODEL\; -t: $Thresh\; Window_size: $Window</font></h4>".'<hr><br><pre>';
for($j=0;$j<@Result;$j++){
if($Result[$j]>= $Thresh){
$EE[$j] = '<a href=" " title="'. $Position[$j].'|'.$PRO[$j].'|'. $Result[$j].'" style="background-color:#FFFFFF;color:#000000;text-decoration:none"><font color="green">E</font></a>';
Expand All @@ -186,7 +192,6 @@
}
}
$Ht=""; #Criteria to exit while

################## Splitting 50 ##########
my (@split_50, $i50);
$i50 = (length($protein)/50);
Expand Down Expand Up @@ -224,8 +229,7 @@
print "Done\n";
#################### Splitting 50 ends###########
#print "$HTML_head @EE";
}
} #While exit
############## HTML Output ENDS #################################
}
################## Protein Mode Ends ########################

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