Phenylketonuria/Task3/Scripts

This script reads an input file in ReProf format or PsiPred and filters the file for the secondary structur presented with H,L and E.
You can find the script in /mnt/home/student/waldraffs/Masterpraktikum/Task3/filter_secStruc.pl

Usage: perl filter_secStrucpl -inp <input-file in ReProf format> -out <output-file> -reprof|-psipred 
-reprof: if the input file is result of a ReProf run
-psipred: if the input file is result of a PsiPred run

The output is the secondary structure shown with the letters E, H and L/C.

Code:

<source lang="perl">

1. !/usr/bin/perl

my $inp; my $out; my $reprof = 0; my $psipred = 0;

1. Reads the command line parameters

for ($i=0; $i<=@ARGV;$i++){ if($ARGV[$i] eq "-inp"){ $inp=$ARGV[$i+1]; } if($ARGV[$i] eq "-out"){ $out=$ARGV[$i+1]; } if($ARGV[$i] eq "-reprof"){ $reprof = 1; } if($ARGV[$i] eq "-psipred"){ $psipred = 1; } }

if(!$inp && !$out){ print "Usage: filter_secStruc.pl -inp <input-file(.reprof)> -out <output-file> -reprof|-psipred" }

my $secstructure= ""; my $no = 0;

1. reads input file and filters for the coloumn with secondary structure

open (FILE,"$inp") || die $!; if($reprof == 1){ while (my $line = <FILE>){

if($no == 1){ @splitLine = split(/\t/,$line); $secstructure="$secstructure$splitLine[2]"; }

if($line =~ /^No/){ $no = 1; } } } if($psipred == 1){ while (my $line = <FILE>){ if($line =~ /^Pred/){ @splitLine = split(/ /,$line); chomp($splitLine[1]); $secstructure = "$secstructure$splitLine[1]"; } } } close FILE;

1. writes output file

open(OUTFILE,">$out") || die $!; print OUTFILE $secstructure; close OUTFILE;

</source>