Question

#!/usr/bin/perl

my $file = $ARGV[0];
my $value = $ARGV[1];

my @grabbed;

open (FILE, $file);

while (<FILE>) {
    if (/alignment#  residue#/) {
            push @grabbed, $_;
            while (<FILE>) {
            last if /^$/;
            push @grabbed, $_;
            }
    }
}
close (FILE);


my $line= `awk '  {if(\$2==$value)} ' @grabbed`;

print $line;

Problem :

1.First, I don’t know if its possible to do awk on an array or not?
2. I am trying to match a value, existing on the second column of the 2-D array (@grabbed). The @grabbed will look like this :

     7         1         M     1.000         6                .VPMLG     66.63
     8         2         S     1.000        10            .QINTSARKG     66.63
     9         3         V     1.000        13         .KTAVFPRGQMSL     66.63
    10         4         L     1.000         7               .SLAKFT     66.63
    11         5         L     1.000        14        .ALSVQWIKMRYPF     66.63
    12         6         R     1.000        16      .DERSAVGTNQLYMIP     66.63
    13         7         S     1.000        18    .GDTHPKRSALFCIQVYN     66.63
    14         8         G     1.000        17     .DRFLENGAQPSTYCHM     66.63
    15         9         L     1.000        19   .NDHPELASVKRCWFGTQI     66.63
    16        10         G     1.000        18    .RLDPEGFTYAVCIKNMH     66.63

I am trying to match and grab the line in which column 2 is of value “9”.

Answer 1

No need to swith to awk when that job can be done with perl too.

for ( @grabbed ) {
    my @f = split;
    if ( $f[1] == $value ) {
        push @line, $_;
    }
}