Shell Programming and Scripting

#!/usr/bin/perl
use strict;

while (<>)
{
        $.<2 and print and next;
          my @f=split/\t/;
         #my @f=split/\s+/;
          my ($FuncIDPrefGene,$AAChangeIDPrefGene,$PopFreqMax,$GeneDetailIDPrefGene,$ClinSig,$Score)=@f[6,11,13,8,46,54];
# Check score for exonic set to 5
         $FuncIDPrefGene eq "exonic" && abs($Score) < 5 and &pj(\@f,"Likely Benign") and next; # Rule 1. Set classification to Likely benign based on score less than 5 for exons

# Check score for everything else set to 5 with GeneDetail following c. nomenclature
        $FuncIDPrefGene !~ "exonic" and abs($Score) < 5 and $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/; # this will capture the digits after    +/- into $1
        $1 < 10 and &pj(\@f,"Likely Benign") and next; # Rule 2. Reclassify intronic variants (with c.) less than 10 based on score

# PopFreqMax VUS
         &pj(\@f,"VUS"); # Rule 3.  If none of the above tests succeeded, and the PopFreqMax < 0.011 set the Classification field to the string VUS.
}
sub pj
{
    my $fr=shift;
       $fr->[55]=shift;
       print join("\t",@{$fr}); # add separator ,"\n"
}

VUS
Likely Benign
Likely Benign

#!/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";

}

perl showme.pl file.txt

$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(.)

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

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

    if (abs($Score) < 5) {
        if($FuncIDPrefGene eq 'exonic') {
            pj(\@f,'Likely Benign');
        }
        else {
            my $scored = $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/;
            pj(\@f, 'Likely Benign') if $scored < 10;
        }
    }
    else {
        pj(\@f, 'VUS');
    }
}
sub pj
{
    my $fr = shift;
    $fr->[55] = shift;
    print join "\t", @{$fr};
}

perl test.pl file.txt 2>/dev/null | perl -naF'\t' -le 'print $F[55]'

Classification
VUS
Likely Benign
Likely Benign

#!/usr/bin/perl    # call perl
use strict;     # use exactdefined criteria
use warnings;   # display warning messages

print scalar <>;  # skip header line
while (<>)    # start conditional checks
{
    my @f = split /\t/;      # split on tabs
    my ( $FuncIDPrefGene,    # field 1
         $AAChangeIDPrefGene, # field 2
         $PopFreqMax,         # field 3
         $GeneDetailIDPrefGene, # field 4
         $ClinSig,              # field 5
         $Score ) = @f[6,11,13,8,46,54];   # field 6 and define field locations using 0 coordinate

    if (abs($Score) < 5) {      # check field 6 for value and ensure its less than 5
        if($FuncIDPrefGene eq 'exonic') {   # check field 1 and if exonic and conditon above met
            pj(\@f,'Likely Benign');    # set field 55 to Likely Benign
        } # end condition 1 block
        else {
            my $scored = $GeneDetailIDPrefGene=~/\.\d+[\+\-](\d+)/;  # use field 4 and split on the . and +/1 and read value into variable
            pj(\@f, 'Likely Benign') if $scored > 10;    # if variable greater then 10 then field 55 is Likely Benign
        }  # end condition 2 block
    } 
    else {
        pj(\@f, 'VUS');  # if niether condition is meet set field 55 to VUS
    }
}  # end while block
sub pj     # define subroutine
{    # start sub block
    my $fr = shift;  # define variable 
    $fr->[55] = shift;  # use field 55 as variable
    print join "\t", @{$fr};   # print value in field
}   # end sub block