Phenylketonuria/Task3/Scripts

This script reads an input file in ReProf format or PsiPred and filters the file for the secondary structur presented with E,H and L/C.
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>