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Top Forums Shell Programming and Scripting Classify lines in file using perl Post 302995599 by Aia on Saturday 8th of April 2017 10:59:56 PM
Old 04-08-2017
Perhaps this might help you:

Code:
#!/usr/bin/perl
use strict;
use warnings;

my $header = scalar <>;
while (<>)
{
    my @f = split /\t/;
    my ( $FuncIDPrefGene,
         $AAChangeIDPrefGene,
         $PopFreqMax,
         $GeneDetailIDPrefGene,
         $ClinSig,
         $Score ) = @f[6,11,13,8,46,54];

     print "\$FuncIDPrefGene = $FuncIDPrefGene and you're trying to abs($Score)\n";

}

Using it with the example you posted it outputs:
Code:
perl showme.pl file.txt

Code:
$FuncIDPrefGene = exonic and you're trying to abs(12)
$FuncIDPrefGene = splicing and you're trying to abs(2)
$FuncIDPrefGene = intronic and you're trying to abs(.)

You have also, precedent issues with the _and_. I suggest you make use of if/else.
This User Gave Thanks to Aia For This Post:
 

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DH_PERL(1)							     Debhelper								DH_PERL(1)

NAME
dh_perl - calculates Perl dependencies and cleans up after MakeMaker SYNOPSIS
dh_perl [debhelperoptions] [-d] [librarydirs...] DESCRIPTION
dh_perl is a debhelper program that is responsible for generating the ${perl:Depends} substitutions and adding them to substvars files. The program will look at Perl scripts and modules in your package, and will use this information to generate a dependency on perl or perlapi. The dependency will be substituted into your package's control file wherever you place the token ${perl:Depends}. dh_perl also cleans up empty directories that MakeMaker can generate when installing Perl modules. OPTIONS
-d In some specific cases you may want to depend on perl-base rather than the full perl package. If so, you can pass the -d option to make dh_perl generate a dependency on the correct base package. This is only necessary for some packages that are included in the base system. Note that this flag may cause no dependency on perl-base to be generated at all. perl-base is Essential, so its dependency can be left out, unless a versioned dependency is needed. -V By default, scripts and architecture independent modules don't depend on any specific version of perl. The -V option causes the current version of the perl (or perl-base with -d) package to be specified. library dirs If your package installs Perl modules in non-standard directories, you can make dh_perl check those directories by passing their names on the command line. It will only check the vendorlib and vendorarch directories by default. CONFORMS TO
Debian policy, version 3.8.3 Perl policy, version 1.20 SEE ALSO
debhelper(7) This program is a part of debhelper. AUTHOR
Brendan O'Dea <bod@debian.org> 11.1.6ubuntu2 2018-05-10 DH_PERL(1)
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