Difference between revisions of "Phenylketonuria/Task3/Scripts"
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The output is the secondary structure shown with the letters E, H and L. |
The output is the secondary structure shown with the letters E, H and L. |
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<source lang="perl"> |
<source lang="perl"> |
Revision as of 16:51, 11 May 2013
This script reads an input file in ReProf format 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>
The output is the secondary structure shown with the letters E, H and L.
Code:
<source lang="perl">
- !/usr/bin/perl
my $inp; my $out;
- Reads the command line parameters
for ($i=0; $i<=3;$i++){ if($ARGV[$i] eq "-inp"){ $inp=$ARGV[$i+1]; }elsif($ARGV[$i] eq "-out"){ $out=$ARGV[$i+1]; } }
if(!$inp && !$out){ print "Usage: filter_secStruc.pl -inp <input-file(.reprof)> -out <output-file>" }
my $secstructure= ""; my $no = 0;
- reads input file and filters for the coloumn with secondary structure
open (FILE,"$inp") || die $!; while (my $line = <FILE>){
if($no == 1){ @splitLine = split(/\t/,$line); $secstructure="$secstructure$splitLine[2]"; }
if($line =~ /^No/){ $no = 1; } } close FILE;
- writes output file
open(OUTFILE,">$out") || die $!; print OUTFILE $secstructure; close OUTFILE;
</source>